[gmx-users] AMBER FF naming and caps

Ebert Maximilian m.ebert at umontreal.ca
Mon Sep 29 16:55:27 CEST 2014

Thank you very much for your help. This answered my questions.

I wish you a great day,

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Montag, 29. September 2014 14:27
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] AMBER FF naming and caps

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The information about manual prefixing is outdated, so we'll need to clean that up.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 http://mackerell.umaryland.edu/~jalemkul

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