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Bug #245

Core dumped with grompp

Added by Mohamed Sherif almost 11 years ago. Updated almost 11 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

Created an attachment (id=310)
structural file that produce the core dumped error.

I am trying grompp, I get 3 different messages, but all with the final line: Aborted (core dumped). Here are some of the outputs:

Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 380 of the 1326 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_1'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA+'
Excluding 1 bonded neighbours molecule type 'CL-'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are: 7124 OTHER residues
There are: 218 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 23639 elements
Making dummy/rest group for Acceleration containing 23639 elements
Making dummy/rest group for Freeze containing 23639 elements
Making dummy/rest group for Energy Mon. containing 23639 elements
Making dummy/rest group for VCM containing 23639 elements
Number of degrees of freedom in T-Coupling group rest is 70917.00
  • glibc detected * grompp: double free or corruption (!prev): 0x0848d9d8 * ======= Backtrace: =========
    /lib/tls/i686/cmov/libc.so.6[0xb7beed65]
    /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7bf2800]
    grompp[0x805d05f] ======= Memory map: ========
    08048000-082ef000 r-xp 00000000 08:05 1091442 /usr/local/bin/grompp
    082ef000-082f6000 rwxp 002a6000 08:05 1091442 /usr/local/bin/grompp
    082f6000-0853a000 rwxp 082f6000 00:00 0 [heap]
    b7600000-b7621000 rwxp b7600000 00:00 0
    b7621000-b7700000 ---p b7621000 00:00 0
    b77ce000-b7830000 rwxp b7830000 00:00 0
    b787d000-b7909000 rwxp b787d000 00:00 0
    b79d9000-b7a22000 rwxp b7b13000 00:00 0
    b7a36000-b7a89000 rwxp b7a66000 00:00 0
    b7a95000-b7ad5000 rwxp b7a95000 00:00 0
    b7ad5000-b7b06000 rwxp b7b05000 00:00 0
    b7b34000-b7b3d000 r-xp 00000000 08:05 1026688 /lib/tls/i686/cmov/libnss_files-2.6.1.so
    b7b3d000-b7b3f000 rwxp 00008000 08:05 1026688 /lib/tls/i686/cmov/libnss_files-2.6.1.so
    b7b3f000-b7b47000 r-xp 00000000 08:05 1029082 /lib/tls/i686/cmov/libnss_nis-2.6.1.so
    b7b47000-b7b49000 rwxp 00007000 08:05 1029082 /lib/tls/i686/cmov/libnss_nis-2.6.1.so
    b7b54000-b7b5e000 r-xp 00000000 08:05 1026275 /lib/libgcc_s.so.1
    b7b5e000-b7b5f000 rwxp 0000a000 08:05 1026275 /lib/libgcc_s.so.1
    b7b5f000-b7b60000 rwxp b7b5f000 00:00 0
    b7b60000-b7b62000 r-xp 00000000 08:05 1026325 /lib/tls/i686/cmov/libdl-2.6.1.so
    b7b62000-b7b64000 rwxp 00001000 08:05 1026325 /lib/tls/i686/cmov/libdl-2.6.1.so
    b7b64000-b7b68000 r-xp 00000000 08:05 17131 /usr/lib/libXdmcp.so.6.0.0
    b7b68000-b7b69000 rwxp 00003000 08:05 17131 /usr/lib/libXdmcp.so.6.0.0
    b7b69000-b7b6b000 r-xp 00000000 08:05 16311 /usr/lib/libXau.so.6.0.0
    b7b6b000-b7b6c000 rwxp 00001000 08:05 16311 /usr/lib/libXau.so.6.0.0
    b7b6c000-b7b6d000 rwxp b7b6c000 00:00 0
    b7b6d000-b7b81000 r-xp 00000000 08:05 1029085 /lib/tls/i686/cmov/libpthread-2.6.1.so
    b7b81000-b7b83000 rwxp 00013000 08:05 1029085 /lib/tls/i686/cmov/libpthread-2.6.1.so
    b7b83000-b7b85000 rwxp b7b83000 00:00 0
    b7b85000-b7cc9000 r-xp 00000000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7cc9000-b7cca000 r-xp 00143000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7cca000-b7ccc000 rwxp 00144000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7ccc000-b7ccf000 rwxp b7ccc000 00:00 0
    b7ccf000-b7dbc000 r-xp 00000000 08:05 17179 /usr/lib/libX11.so.6.2.0
    b7dbc000-b7dc0000 rwxp 000ed000 08:05 17179 /usr/lib/libX11.so.6.2.0
    b7dc0000-b7dd5000 r-xp 00000000 08:05 18960 /usr/lib/libICE.so.6.3.0
    b7dd5000-b7dd7000 rwxp 00014000 08:05 18960 /usr/lib/libICE.so.6.3.0
    b7dd7000-b7dd8000 rwxp b7dd7000 00:00 0
    b7dd8000-b7ddf000 r-xp 00000000 08:05 17778 /usr/lib/libSM.so.6.0.0
    b7ddf000-b7de0000 rwxp 00006000 08:05 17778 /usr/lib/libSM.so.6.0.0
    b7de0000-b7e03000 r-xp 00000000 08:05 1026326 /lib/tls/i686/cmov/libm-2.6.1.so
    b7e03000-b7e05000 rwxp 00023000 08:05 1026326 /lib/tls/i686/cmov/libm-2.6.1.so
    b7e05000-b7e06000 rwxp b7e05000 00:00 0
    b7e06000-b7edd000 r-xp 00000000 08:05 343395 /usr/lib/libfftw3f.so.3.1.2
    b7edd000-b7ee3000 rwxp 000d7000 08:05 343395 /usr/lib/libfftw3f.so.3.1.2
    b7ee3000-b7ef7000 r-xp 00000000 08:05 1026328 /lib/tls/i686/cmov/libnsl-2.6.1.so
    b7ef7000-b7ef9000 rwxp 00013000 08:05 1026328 /lib/tls/i686/cmov/libnsl-2.6.1.so
    b7ef9000-b7efb000 rwxp b7ef9000 00:00 0
    b7eff000-b7f06000 r-xp 00000000 08:05 1026329 /lib/tls/i686/cmov/libnss_compat-2.6.1.so
    b7f06000-b7f08000 rwxp 00006000 08:05 1026329 /lib/tls/i686/cmov/libnss_compat-2.6.1.so
    b7f10000-b7f13000 rwxp b7f10000 00:00 0
    b7f13000-b7f2d000 r-xp 00000000 08:Aborted (core dumped)

Another one is:
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 380 of the 1326 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_1'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA+'
Excluding 1 bonded neighbours molecule type 'CL-'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are: 7124 OTHER residues
There are: 218 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 23639 elements
Making dummy/rest group for Acceleration containing 23639 elements
Making dummy/rest group for Freeze containing 23639 elements
Making dummy/rest group for Energy Mon. containing 23639 elements
Making dummy/rest group for VCM containing 23639 elements
Number of degrees of freedom in T-Coupling group rest is 70917.00
  • glibc detected * grompp: double free or corruption (!prev): 0x0848d9d8 * ======= Backtrace: =========
    /lib/tls/i686/cmov/libc.so.6[0xb7bd5d65]
    /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7bd9800]
    grompp[0x805d05f] ======= Memory map: ========
    08048000-082ef000 r-xp 00000000 08:05 1091442 /usr/local/bin/grompp
    082ef000-082f6000 rwxp 002a6000 08:05 1091442 /usr/local/bin/grompp
    082f6000-0853a000 rwxp 082f6000 00:00 0 [heap]
    b7600000-b7621000 rwxp b7600000 00:00 0
    b7621000-b7700000 ---p b7621000 00:00 0
    b77b5000-b7817000 rwxp b7817000 00:00 0
    b7864000-b78f0000 rwxp b7864000 00:00 0
    b79c0000-b7a09000 rwxp b7afa000 00:00 0
    b7a1d000-b7a70000 rwxp b7a4d000 00:00 0
    b7a7c000-b7abc000 rwxp b7a7c000 00:00 0
    b7abc000-b7aed000 rwxp b7aec000 00:00 0
    b7b1b000-b7b24000 r-xp 00000000 08:05 1026688 /lib/tls/i686/cmov/libnss_files-2.6.1.so
    b7b24000-b7b26000 rwxp 00008000 08:05 1026688 /lib/tls/i686/cmov/libnss_files-2.6.1.so
    b7b26000-b7b2e000 r-xp 00000000 08:05 1029082 /lib/tls/i686/cmov/libnss_nis-2.6.1.so
    b7b2e000-b7b30000 rwxp 00007000 08:05 1029082 /lib/tls/i686/cmov/libnss_nis-2.6.1.so
    b7b3b000-b7b45000 r-xp 00000000 08:05 1026275 /lib/libgcc_s.so.1
    b7b45000-b7b46000 rwxp 0000a000 08:05 1026275 /lib/libgcc_s.so.1
    b7b46000-b7b47000 rwxp b7b46000 00:00 0
    b7b47000-b7b49000 r-xp 00000000 08:05 1026325 /lib/tls/i686/cmov/libdl-2.6.1.so
    b7b49000-b7b4b000 rwxp 00001000 08:05 1026325 /lib/tls/i686/cmov/libdl-2.6.1.so
    b7b4b000-b7b4f000 r-xp 00000000 08:05 17131 /usr/lib/libXdmcp.so.6.0.0
    b7b4f000-b7b50000 rwxp 00003000 08:05 17131 /usr/lib/libXdmcp.so.6.0.0
    b7b50000-b7b52000 r-xp 00000000 08:05 16311 /usr/lib/libXau.so.6.0.0
    b7b52000-b7b53000 rwxp 00001000 08:05 16311 /usr/lib/libXau.so.6.0.0
    b7b53000-b7b54000 rwxp b7b53000 00:00 0
    b7b54000-b7b68000 r-xp 00000000 08:05 1029085 /lib/tls/i686/cmov/libpthread-2.6.1.so
    b7b68000-b7b6a000 rwxp 00013000 08:05 1029085 /lib/tls/i686/cmov/libpthread-2.6.1.so
    b7b6a000-b7b6c000 rwxp b7b6a000 00:00 0
    b7b6c000-b7cb0000 r-xp 00000000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7cb0000-b7cb1000 r-xp 00143000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7cb1000-b7cb3000 rwxp 00144000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7cb3000-b7cb6000 rwxp b7cb3000 00:00 0
    b7cb6000-b7da3000 r-xp 00000000 08:05 17179 /usr/lib/libX11.so.6.2.0
    b7da3000-b7da7000 rwxp 000ed000 08:05 17179 /usr/lib/libX11.so.6.2.0
    b7da7000-b7dbc000 r-xp 00000000 08:05 18960 /usr/lib/libICE.so.6.3.0
    b7dbc000-b7dbe000 rwxp 00014000 08:05 18960 /usr/lib/libICE.so.6.3.0
    b7dbe000-b7dbf000 rwxp b7dbe000 00:00 0
    b7dbf000-b7dc6000 r-xp 00000000 08:05 17778 /usr/lib/libSM.so.6.0.0
    b7dc6000-b7dc7000 rwxp 00006000 08:05 17778 /usr/lib/libSM.so.6.0.0
    b7dc7000-b7dea000 r-xp 00000000 08:05 1026326 /lib/tls/i686/cmov/libm-2.6.1.so
    b7dea000-b7dec000 rwxp 00023000 08:05 1026326 /lib/tls/i686/cmov/libm-2.6.1.so
    b7dec000-b7ded000 rwxp b7dec000 00:00 0
    b7ded000-b7ec4000 r-xp 00000000 08:05 343395 /usr/lib/libfftw3f.so.3.1.2
    b7ec4000-b7eca000 rwxp 000d7000 08:05 343395 /usr/lib/libfftw3f.so.3.1.2
    b7eca000-b7ede000 r-xp 00000000 08:05 1026328 /lib/tls/i686/cmov/libnsl-2.6.1.so
    b7ede000-b7ee0000 rwxp 00013000 08:05 1026328 /lib/tls/i686/cmov/libnsl-2.6.1.so
    b7ee0000-b7ee2000 rwxp b7ee0000 00:00 0
    b7ee6000-b7eed000 r-xp 00000000 08:05 1026329 /lib/tls/i686/cmov/libnss_compat-2.6.1.so
    b7eed000-b7eef000 rwxp 00006000 08:05 1026329 /lib/tls/i686/cmov/libnss_compat-2.6.1.so
    b7ef7000-b7efa000 rwxp b7ef7000 00:00 0
    b7efa000-b7f14000 r-xp 00000000 08:05 1029444 /lib/lAborted (core dumped)

A third one is:Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 380 of the 1326 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_1'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA+'
Excluding 1 bonded neighbours molecule type 'CL-'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are: 7124 OTHER residues
There are: 218 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 23639 elements
Making dummy/rest group for Acceleration containing 23639 elements
Making dummy/rest group for Freeze containing 23639 elements
Making dummy/rest group for Energy Mon. containing 23639 elements
Making dummy/rest group for VCM containing 23639 elements
Number of degrees of freedom in T-Coupling group rest is 70917.00
  • glibc detected * grompp: double free or corruption (!prev): 0x0848d9d8 * ======= Backtrace: =========
    /lib/tls/i686/cmov/libc.so.6[0xb7cadd65]
    /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7cb1800]
    grompp[0x805d05f] ======= Memory map: ========
    08048000-082ef000 r-xp 00000000 08:05 1091442 /usr/local/bin/grompp
    082ef000-082f6000 rwxp 002a6000 08:05 1091442 /usr/local/bin/grompp
    082f6000-0853a000 rwxp 082f6000 00:00 0 [heap]
    b7700000-b7721000 rwxp b7700000 00:00 0
    b7721000-b7800000 ---p b7721000 00:00 0
    b788d000-b78ef000 rwxp b78ef000 00:00 0
    b793c000-b79c8000 rwxp b793c000 00:00 0
    b7a98000-b7ae1000 rwxp b7bd2000 00:00 0
    b7af5000-b7b48000 rwxp b7b25000 00:00 0
    b7b54000-b7b94000 rwxp b7b54000 00:00 0
    b7b94000-b7bc5000 rwxp b7bc4000 00:00 0
    b7bf3000-b7bfc000 r-xp 00000000 08:05 1026688 /lib/tls/i686/cmov/libnss_files-2.6.1.so
    b7bfc000-b7bfe000 rwxp 00008000 08:05 1026688 /lib/tls/i686/cmov/libnss_files-2.6.1.so
    b7bfe000-b7c06000 r-xp 00000000 08:05 1029082 /lib/tls/i686/cmov/libnss_nis-2.6.1.so
    b7c06000-b7c08000 rwxp 00007000 08:05 1029082 /lib/tls/i686/cmov/libnss_nis-2.6.1.so
    b7c13000-b7c1d000 r-xp 00000000 08:05 1026275 /lib/libgcc_s.so.1
    b7c1d000-b7c1e000 rwxp 0000a000 08:05 1026275 /lib/libgcc_s.so.1
    b7c1e000-b7c1f000 rwxp b7c1e000 00:00 0
    b7c1f000-b7c21000 r-xp 00000000 08:05 1026325 /lib/tls/i686/cmov/libdl-2.6.1.so
    b7c21000-b7c23000 rwxp 00001000 08:05 1026325 /lib/tls/i686/cmov/libdl-2.6.1.so
    b7c23000-b7c27000 r-xp 00000000 08:05 17131 /usr/lib/libXdmcp.so.6.0.0
    b7c27000-b7c28000 rwxp 00003000 08:05 17131 /usr/lib/libXdmcp.so.6.0.0
    b7c28000-b7c2a000 r-xp 00000000 08:05 16311 /usr/lib/libXau.so.6.0.0
    b7c2a000-b7c2b000 rwxp 00001000 08:05 16311 /usr/lib/libXau.so.6.0.0
    b7c2b000-b7c2c000 rwxp b7c2b000 00:00 0
    b7c2c000-b7c40000 r-xp 00000000 08:05 1029085 /lib/tls/i686/cmov/libpthread-2.6.1.so
    b7c40000-b7c42000 rwxp 00013000 08:05 1029085 /lib/tls/i686/cmov/libpthread-2.6.1.so
    b7c42000-b7c44000 rwxp b7c42000 00:00 0
    b7c44000-b7d88000 r-xp 00000000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7d88000-b7d89000 r-xp 00143000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7d89000-b7d8b000 rwxp 00144000 08:05 1026322 /lib/tls/i686/cmov/libc-2.6.1.so
    b7d8b000-b7d8e000 rwxp b7d8b000 00:00 0
    b7d8e000-b7e7b000 r-xp 00000000 08:05 17179 /usr/lib/libX11.so.6.2.0
    b7e7b000-b7e7f000 rwxp 000ed000 08:05 17179 /usr/lib/libX11.so.6.2.0
    b7e7f000-b7e94000 r-xp 00000000 08:05 18960 /usr/lib/libICE.so.6.3.0
    b7e94000-b7e96000 rwxp 00014000 08:05 18960 /usr/lib/libICE.so.6.3.0
    b7e96000-b7e97000 rwxp b7e96000 00:00 0
    b7e97000-b7e9e000 r-xp 00000000 08:05 17778 /usr/lib/libSM.so.6.0.0
    b7e9e000-b7e9f000 rwxp 00006000 08:05 17778 /usr/lib/libSM.so.6.0.0
    b7e9f000-b7ec2000 r-xp 00000000 08:05 1026326 /lib/tls/i686/cmov/libm-2.6.1.so
    b7ec2000-b7ec4000 rwxp 00023000 08:05 1026326 /lib/tls/i686/cmov/libm-2.6.1.so
    b7ec4000-b7ec5000 rwxp b7ec4000 00:00 0
    b7ec5000-b7f9c000 r-xp 00000000 08:05 343395 /usr/lib/libfftw3f.so.3.1.2
    b7f9c000-b7fa2000 rwxp 000d7000 08:05 343395 /usr/lib/libfftw3f.so.3.1.2
    b7fa2000-b7fb6000 r-xp 00000000 08:05 1026328 /lib/tls/i686/cmov/libnsl-2.6.1.so
    b7fb6000-b7fb8000 rwxp 00013000 08:05 1026328 /lib/tls/i686/cmov/libnsl-2.6.1.so
    b7fb8000-b7fba000 rwxp b7fb8000 00:00 0
    b7fbe000-b7fc5000 r-xp 00000000 08:05 1026329 /lib/tls/i686/cmov/libnss_compat-2.6.1.so
    b7fc5000-b7fc7000 rwxp 00006000 08:05 1026329 /lib/tls/i686/cmov/libnss_compat-2.6.1.so
    b7fcf000-b7fd2000 rwxp b7fcf000 00:00 0
    b7fd2000-b7fec000 r-xp 00000000 08:05 1029444 /lib/ld-2.6.1.so
    b7fec000-b7fee000 rwxp 00019000 08:05 1029444 /lib/ld-2.6.1.so
    bfc8f000-bfca4000 rwxp bfc8f000 00:00 0 [stack]
    ffffe000-fffff000 r-xp 00000000 00:00 0 [vdso]
    Aborted (core dumped)

My system consists of a globular protin with another peptide (alpha helix) bound to a groove. The globular protein has 2 Ca++ ions. The total charge of the system is -6 e, so I added 6 NA+ ions, using teh genion. Here is the .mdp file for grompp to generate the .tpr file for genion:

; VARIOUS PREPROCESSING OPTIONS =
title = For genion
cpp = /usr/bin/cpp
include =
define = -DFLEXIBLE

That's all. Could there be something missing in the file that is causing the problem? However, the genion runs, and 2 files are generated. It is these 2 files that produce the error when I try to run an energy minimization simulation.

I am attaching the files to the report.

Thank you in advance for your kind help.

mution.gro (1.01 MB) mution.gro structural file that produce the core dumped error. Mohamed Sherif, 11/02/2008 03:05 AM
mutopol.top (778 Bytes) mutopol.top This is the topology file. Mohamed Sherif, 11/02/2008 03:06 AM
mutem.mdp (493 Bytes) mutem.mdp This is the mdp file for energy minimization that I used. Mohamed Sherif, 11/02/2008 03:07 AM
mutopol_A.itp (450 KB) mutopol_A.itp This is the topology file for the globular protein. Mohamed Sherif, 11/03/2008 03:33 PM
mutopol_1.itp (58.3 KB) mutopol_1.itp This is the topology file for the alpha helix. Mohamed Sherif, 11/03/2008 03:34 PM

History

#1 Updated by Mohamed Sherif almost 11 years ago

Created an attachment (id=311)
This is the topology file.

#2 Updated by Mohamed Sherif almost 11 years ago

Created an attachment (id=312)
This is the mdp file for energy minimization that I used.

That's all. Thank you.

#3 Updated by Berk Hess almost 11 years ago

You need to also attach to itp files:
#include "mutopol_A.itp"
#include "mutopol_1.itp"

Berk

#4 Updated by Mohamed Sherif almost 11 years ago

Created an attachment (id=318)
This is the topology file for the globular protein.

#5 Updated by Mohamed Sherif almost 11 years ago

Created an attachment (id=319)
This is the topology file for the alpha helix.

#6 Updated by Mohamed Sherif almost 11 years ago

I think that I did not understand what did you mean. Did you mean for me to attahc those files? I attached them. Or do you mean that you need me to include within a certain file? If this is the case, then which?

Thank you in advance for your help.

#7 Updated by Berk Hess almost 11 years ago

The crash is caused by the last line of you top file
where you add 0 Cl- molecules.
I have fixed the bug for the next release.
You can make grompp work for now for your case by removing
this line with 0 molecules.

Berk

#8 Updated by Mohamed Sherif almost 11 years ago

Thanks. This did solve the problem. Sorry for the delay.
Thanks again.

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