[gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 78

[amitbehra at chemeng.iisc.ernet.in]

Hello Justin,
I used gmx pdb2gmx -f protein.pdb -o protein.gro -ignh

and I got the error:
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/home/amit/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/pgutil.c,
line: 127

Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

Regards,
Amit Behera

> ------------------------------
>
> Message: 7
> Date: Fri, 19 Aug 2016 15:30:14 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] pdb2gmx
> Message-ID: <d8bcd9d8-b628-8e61-70e6-42e2dcca99da at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 8/19/16 10:52 AM, amitbehra at chemeng.iisc.ernet.in wrote:
>> Hello users,
>> I am using pdb2gmx on a protein.
>> Fatal error:
>> Residue 1 named LYS of a molecule in the input file was mapped
>> to an entry in the topology database, but the atom N used in
>> that entry is not found in the input file. Perhaps your atom
>> and/or residue naming needs to be fixed.
>>
>> ATOM      1  N   LYS     8      59.565  44.696  51.226  1.00  0.00
>>   N
>> 0.00           H
>> ATOM     19  NZ  LYS     8      62.201  50.111  51.767  1.00  0.00
>>   N
>>
>> These are N atoms in my LYS . Can anyone point out what the problem.
>>
>
> Please provide your exact pdb2gmx command and the full screen output.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================