gromacs 5 pdb2gmx doesn't pick up multiple torsions additive torsions in AMBER99sb-ILDN
For the AMBER99sb-ILDN force field, the gromacs aminoacids.rtp file contains multiple dihedrals (the extra ones added for ILDN) as torsion definitions like this in both gromacs versions 4.6.7 and 5.0.5:
N CA CB CG2 torsion_ILE_N_CA_CB_CG2_mult1
N CA CB CG2 torsion_ILE_N_CA_CB_CG2_mult2
C CA CB CG torsion_ASN_C_CA_CB_CG_mult1
C CA CB CG torsion_ASN_C_CA_CB_CG_mult2
C CA CB CG torsion_ASN_C_CA_CB_CG_mult3
C CA CB CG torsion_ASN_C_CA_CB_CG_mult4
C CA CB CG torsion_ASN_C_CA_CB_CG_mult5
C CA CB CG torsion_ASN_C_CA_CB_CG_mult6
CA CB CG ND2 torsion_ASN_CA_CB_CG_ND2_mult1
CA CB CG ND2 torsion_ASN_CA_CB_CG_ND2_mult2
CA CB CG ND2 torsion_ASN_CA_CB_CG_ND2_mult3
CA CB CG ND2 torsion_ASN_CA_CB_CG_ND2_mult4
CA CB CG ND2 torsion_ASN_CA_CB_CG_ND2_mult5
CA CB CG ND2 torsion_ASN_CA_CB_CG_ND2_mult6
However, while gromacs 4.6.7 pdb2gmx picks up all of these torsions correctly, gromacs 5.0.5 pdb2gmx appears to pick up only the first one. Therefore, ILE omits torsion_ILE_N_CA_CB_CG2_mult2 and ASN omits a total of 10 torsion terms.
My understanding from looking at the .top file output from pdb2gmx is that gromacs 5.0.5 pdb2gmx is not giving the user the correct force field.
For an AIA peptide:
$ diff gmx4.6.7.top gmx5.0.5.top|grep torsion
< 13 15 17 19 9 torsion_ILE_N_CA_CB_CG2_mult2
For an ANA peptide:
gpc-logindm01-ib0-$ diff gmx4.6.7.top gmx5.0.5.top|grep torsion
< 25 15 17 20 9 torsion_ASN_C_CA_CB_CG_mult2
< 25 15 17 20 9 torsion_ASN_C_CA_CB_CG_mult3
< 25 15 17 20 9 torsion_ASN_C_CA_CB_CG_mult4
< 25 15 17 20 9 torsion_ASN_C_CA_CB_CG_mult5
< 25 15 17 20 9 torsion_ASN_C_CA_CB_CG_mult6
< 15 17 20 22 9 torsion_ASN_CA_CB_CG_ND2_mult2
< 15 17 20 22 9 torsion_ASN_CA_CB_CG_ND2_mult3
< 15 17 20 22 9 torsion_ASN_CA_CB_CG_ND2_mult4
< 15 17 20 22 9 torsion_ASN_CA_CB_CG_ND2_mult5
< 15 17 20 22 9 torsion_ASN_CA_CB_CG_ND2_mult6
These differences persist in the processed topology that I get from grompp -pp
I have also checked gromacs 5.0.4 and it behaves the same way as gromacs 5.0.5.
I have attached a tarball of my testing for the AIA and ANA peptides. You will need to change two lines in run.sh where gromacs is placed in the PATH and GMXLIB is set (I currently have ". ~/.gmx4.6.7" or ". ~/.gmx5.0.5" to set these up).
#3 Updated by Teemu Murtola over 4 years ago
- Project changed from Support Platforms to GROMACS
- Category set to preprocessing (pdb2gmx,grompp)
- Status changed from New to Feedback wanted
- Affected version changed from current to 5.0.5
This looks like an exact duplicate of several other already reported issues.
PS. The Support Platforms project is not for reporting Gromacs bugs, but for tracking issues that affect the infrastructure that supports Gromacs development (e.g., Redmine or continuous integration build machines).
#4 Updated by Chris Neale over 4 years ago
Agreed it is a duplicate. Sorry.
With respect to the "support platforms" vs "gromacs bugs", I am not aware that I selected support platforms. As I recall, I went here http://redmine.gromacs.org/projects/gromacs/issues/new and tried to add a new issue.