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Bug #587

Updated by Rossen Apostolov over 8 years ago

I have tried to calculate the vsites with the option aromatic using charmm27 and no solvent and have hit a problem with the amino acid tyrosine.



to repeat the bug:



pdb2gmx -f test.gro -vsite aromatic -ignh -ff charmm27 -water none



...



Identified residue TYR2 as a starting terminus.

Identified residue TYR2 as a ending terminus.

8 out of 8 lines of specbond.dat converted successfully

Start terminus: NH3+

End terminus: COO-

Opening force field file /opt/gromacs45/share/gromacs/top/charmm27.ff/aminoacids.arn

Checking for duplicate atoms....

Now there are 1 residues with 24 atoms

Making bonds...

Number of bonds was 24, now 24



-------------------------------------------------------

Program pdb2gmx, VERSION 4.5.1

Source code file: gen_vsite.c, line: 445



Fatal error:

Dummy mass type (MW) not found in atom type database

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------



...



here is the file test.gro



Test

21

2TYR N 927 5.792 -7.649 0.694

2TYR H 928 5.790 -7.742 0.660

2TYR CA 929 5.669 -7.568 0.690

2TYR HA 930 5.701 -7.474 0.698

2TYR CB 931 5.595 -7.591 0.559

2TYR HB1 932 5.587 -7.690 0.541

2TYR HB2 933 5.503 -7.551 0.564

2TYR CG 934 5.671 -7.527 0.446

2TYR CD1 935 5.661 -7.388 0.427

2TYR HD1 936 5.605 -7.333 0.488

2TYR CE1 937 5.731 -7.327 0.322

2TYR HE1 938 5.725 -7.229 0.308

2TYR CZ 939 5.810 -7.405 0.237

2TYR OH 940 5.879 -7.345 0.133

2TYR HH 941 5.930 -7.415 0.082

2TYR CD2 942 5.749 -7.604 0.361

2TYR HD2 943 5.756 -7.703 0.375

2TYR CE2 944 5.819 -7.543 0.256

2TYR HE2 945 5.876 -7.599 0.195

2TYR C 946 5.576 -7.603 0.806

2TYR O 947 5.459 -7.565 0.805

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