[gmx-users] GROMOS 54a7 mapping warning
Justin Lemkul
jalemkul at vt.edu
Thu Aug 1 16:09:18 CEST 2019
On 8/1/19 6:25 AM, Gselman, Larissa wrote:
> 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?
Using -ignh should be fine. The warnings are just pdb2gmx being (in my
opinion) too noisy. It is telling you that it is applying patches to
remove those atoms, which is actually what you want. A warning should
not prevent the topology from being written. If it is, you can move on.
-Justin
>
> 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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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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jalemkul at vt.edu | (540) 231-3129
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