[gmx-users] GROMOS 54a7 mapping warning
Gselman, Larissa
larissa.gselman at rwth-aachen.de
Thu Aug 1 12:25:44 CEST 2019
Thank you for your answer! I used the Yasara -> Edit -> Clean Option and it added atoms (1H, 2H and 3H for ASP and OXT for ASN) to my pdb file.
Nevertheless, I still get the same warnings when I try with -ignh. I cannot see that there are other atoms missing?
When I try without -ignh, I even get a fatal error which says: Atom HA in residue ASP 1 was not found in rtp entry ASP with 11 atoms while sorting atoms.
When I look into the aminoacids.rtp file from the GROMOS 54a7 force field it looks like this:
[ ASP ]
[ atoms ]
N N -0.31000 0
H H 0.31000 0
CA CH1 0.00000 1
CB CH2 0.00000 1
CG C 0.27000 2
OD1 OM -0.63500 2
OD2 OM -0.63500 2
C C 0.450 3
O O -0.450 3
Here are my first and last amino acids from the new pdb file with the added atoms:
ATOM 1 N ASP A 1 59.994 60.432 82.286 1.00 7.49 N
ATOM 2 1H ASP A 1 60.547 59.791 81.754 1.00 7.49 H
ATOM 3 2H ASP A 1 59.319 59.903 82.801 1.00 7.49 H
ATOM 4 3H ASP A 1 60.596 60.885 82.944 1.00 7.49 H
ATOM 5 CA ASP A 1 59.341 61.407 81.415 1.00 7.49 C
ATOM 6 HA ASP A 1 58.651 60.833 80.799 1.00 7.49 H
ATOM 7 C ASP A 1 60.313 62.117 80.435 1.00 7.49 C
ATOM 8 O ASP A 1 61.524 61.881 80.391 1.00 7.49 O
ATOM 9 CB ASP A 1 58.494 62.384 82.263 1.00 7.49 C
ATOM 10 1HB ASP A 1 58.142 61.868 83.157 1.00 7.49 H
ATOM 11 2HB ASP A 1 59.114 63.222 82.584 1.00 7.49 H
ATOM 12 CG ASP A 1 57.247 62.920 81.535 1.00 7.49 C
ATOM 13 OD1 ASP A 1 57.107 62.729 80.305 1.00 7.49 O
ATOM 14 OD2 ASP A 1 56.369 63.525 82.180 1.00 7.49 O
.
.
.
ATOM 626 N ASN A 38 49.792 47.722 37.078 1.00 13.81 N
ATOM 627 H ASN A 38 50.649 48.244 36.922 1.00 13.81 H
ATOM 628 CA ASN A 38 48.636 48.172 36.306 1.00 13.81 C
ATOM 629 HA ASN A 38 48.705 49.256 36.233 1.00 13.81 H
ATOM 630 C ASN A 38 47.283 47.875 36.982 1.00 13.81 C
ATOM 631 O ASN A 38 47.185 47.311 38.072 1.00 13.81 O
ATOM 632 OXT ASN A 38 46.199 48.179 36.482 1.00 13.81 O
ATOM 633 CB ASN A 38 48.757 47.594 34.881 1.00 13.81 C
ATOM 634 1HB ASN A 38 47.934 47.954 34.264 1.00 13.81 H
ATOM 635 2HB ASN A 38 49.688 47.938 34.433 1.00 13.81 H
ATOM 636 CG ASN A 38 48.756 46.074 34.842 1.00 13.81 C
ATOM 637 OD1 ASN A 38 49.775 45.434 34.642 1.00 13.81 O
ATOM 638 ND2 ASN A 38 47.621 45.445 35.027 1.00 13.81 N
ATOM 639 1HD2 ASN A 38 47.668 44.445 35.083 1.00 13.81 H
ATOM 640 2HD2 ASN A 38 46.815 45.983 35.313 1.00 13.81 H
TER 641 ASN A 38
END
Thank you so much for your help.
________________________________
Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> im Auftrag von David van der Spoel <spoel at xray.bmc.uu.se>
Gesendet: Mittwoch, 31. Juli 2019 21:21:39
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] GROMOS 54a7 mapping warning
Den 2019-07-31 kl. 15:21, skrev Gselman, Larissa:
> Hallo everyone,
>
>
> I want to simulate a peptide with the Gromos 54a7 force field.
Your structure is missing atoms, please fix and rerun without -ignh.
>
>
> So, my first command is:
>
> gmx_mpi pdb2gmx -f Mh.pdb -o Mh_processed.gro -water spce -ignh -inter
>
> I choose 14 for the Gromos 54a7 ff, then I choose the protonation state the titratable amino acids and for the termini I choose the zwitterionic state (so I choose 0 and 0).
>
> But this results in the following warnings:
>
> WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.
>
> WARNING: WARNING: Residue 38 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.
>
>
> This is the beginning and end of my pdb file with ASP as first and ASN as last amino acid:
>
> ATOM 1 N ASP A 1 59.994 60.432 82.286 1.00 7.49
> ATOM 2 CA ASP A 1 59.341 61.407 81.415 1.00 7.49
> ATOM 3 HA ASP A 1 58.651 60.833 80.799 1.00 7.49
> ATOM 4 CB ASP A 1 58.494 62.384 82.263 1.00 7.49
> ATOM 5 HB1 ASP A 1 59.114 63.222 82.584 1.00 7.49
> ATOM 6 HB2 ASP A 1 58.142 61.868 83.157 1.00 7.49
> ATOM 7 CG ASP A 1 57.247 62.920 81.535 1.00 7.49
> ATOM 8 OD1 ASP A 1 57.107 62.729 80.305 1.00 7.49
> ATOM 9 OD2 ASP A 1 56.369 63.525 82.180 1.00 7.49
> ATOM 10 C ASP A 1 60.313 62.117 80.435 1.00 7.49
> ATOM 11 O ASP A 1 61.524 61.881 80.391 1.00 7.49
> .
> .
> .
> ATOM 623 N ASN A 38 49.792 47.722 37.078 1.00 13.81
> ATOM 624 H ASN A 38 50.649 48.244 36.922 1.00 13.81
> ATOM 625 CA ASN A 38 48.636 48.172 36.306 1.00 13.81
> ATOM 626 HA ASN A 38 48.705 49.256 36.233 1.00 13.81
> ATOM 627 CB ASN A 38 48.757 47.594 34.881 1.00 13.81
> ATOM 628 HB1 ASN A 38 49.688 47.938 34.433 1.00 13.81
> ATOM 629 HB2 ASN A 38 47.934 47.954 34.264 1.00 13.81
> ATOM 630 CG ASN A 38 48.756 46.074 34.842 1.00 13.81
> ATOM 631 OD1 ASN A 38 49.775 45.434 34.642 1.00 13.81
> ATOM 632 ND2 ASN A 38 47.621 45.445 35.027 1.00 13.81
> ATOM 633 1HD2 ASN A 38 46.815 45.983 35.313 1.00 13.81
> ATOM 634 2HD2 ASN A 38 47.668 44.445 35.083 1.00 13.81
> ATOM 635 C ASN A 38 47.283 47.875 36.982 1.00 13.81
> ATOM 636 O ASN A 38 47.185 47.311 38.072 1.00 13.81
> TER
>
>
> I hope you can help me and maybe tell me why this problem occurs and what I have to change. Thank you very much!
>
> Best regards
> Larissa
>
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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