[gmx-users] AMBER FF naming and caps
jalemkul at vt.edu
Mon Sep 29 14:26:59 CEST 2014
On 9/29/14 5:58 AM, Ebert Maximilian wrote:
> Dear list,
> I am a little bit confused regarding the preparation needed to use the AMBER FF in GROMACS 5.0.1. I have a simple PDB file of a protein and I use this as input to pdb2gmx. I selected the AMBER FF during the creation process:
> gmx_mpi pdb2gmx -f protein.pdb -o protein_processed.gro -water spce
> This generates the gro, top and itp file. Now when I open the gro file in VMD I get an unusual bond between the last two residues of the protein chain. I already figured out why this is. The last amino acid has a charged carboxylate with the atom type OC1 and OC2 which are not identified as amino acids by VMD. After further reading of the manual I found this paragraph:
> The AMBER force fields have unique forms for the terminal residues, and these are incompatible with the -ter mechanism. You need to prefix your N- or C-terminal residue names with "N" or "C" respectively to use these forms, making sure you preserve the format of the coordinate file. Alternatively, use named terminating residues (e.g. ACE, NME).
> Now I was thinking that I have to change the name of the N and C terminal residue. However, looking into my top file GROMACS already knows about AMBER's naming convention:
> ; residue 290 TRP rtp CTRP q -1.0
> 4049 N 290 TRP N 4049 -0.3821 14.01 ; qtot -6.382
> 4050 H 290 TRP H 4050 0.2681 1.008 ; qtot -6.114
> 4051 CT 290 TRP CA 4051 -0.2084 12.01 ; qtot -6.322
> Now my question do I have to do anything or is GROMACS 5 taking care of the correct termini in the AMBERE FF?
The information about manual prefixing is outdated, so we'll need to clean that
up. Bonds drawn in VMD are not definitive, but those in the topology are. If
you have multiple chains and the bonded structure in the topology is correct,
then there's no problem.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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