[gmx-users] Fix the residues

[Justin Lemkul]

On 1/6/17 1:58 PM, liming_52 wrote:
> Dear Gromacs users,
>
> I am trying to run a md using 4n6p.cif, which was obtained from PDB. I converted the file into pdb format using DS4.1, and got the file named lactoferrin.pdb. When I directly run
> the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce", the program runs and produces the information as follows:
> ...

You snipped out the most important information.  Please provide the full screen 
output from pdb2gmx.

-Justin

> WARNING: WARNING: Residue 1 named TYR 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 335 named SER 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.
>
> ...
> How should I fix the residues? And which tools should I use? Is there any examples or tutorials?
>
> If anyone can suggest a solution to this issue, it would be really helpful.
>
>
>
>
>
>
>
> --
>
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China
>

-- 
==================================================

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

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