[gmx-users] adding a new atom type

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jul 25 13:58:21 CEST 2012

 Some time ago I defined a new residue and after running grompp I got an error as there are some interactions assigned multiple times. Then I decided to duplicate the atoms involved in that residue to avoid this error.
Next I renamed the atomtypes in atometypes.atp as below:
 ZC    12.01100 ;    carbonyl C, peptide backbone 
ZCT1    12.01100 ;    aliphatic sp3 C for CH 
ZCT3    12.01100 ;    aliphatic sp3 C for CH3 
ZO    15.99900 ;    carbonyl oxygen 
ZHC    1.00800 ;    N-ter H 
ZNH1    14.00700 ;    peptide nitrogen 
ZH    1.00800 ;    polar H 
ZHB    1.00800 ;    backbone H 
ZHA    1.00800 ;    nonpolar H 

Then I wanted to modify the .itp file, got in to the trouble; I couldn't find the C atomtype in nonbonded.itp file. Actually I don't know what to do now! 

Thanks for your suggestions.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, July 25, 2012 4:20 PM
Subject: Re: [gmx-users] adding a new atom type

On 7/25/12 7:30 AM, Shima Arasteh wrote:
> Hi,
> The force field which I am using is CHARMM36.
> I added some new atom types to the atomtypes.atp .  Then I need to change the nonbonded.itp file. Are the atom names are used in .itp files? So how I find a last-defined atom types in the .itp file?

An "atom name" and an "atom type" are distinct concepts.  The atoms that are named in the topology must have atom types that are defined in ffnonbonded.itp.  Names are convenient labels and are irrelevant except for our own understanding of the content of our files; types define the nature of the interactions the atom experiences.  Parameters are assigned in the topology based on atom type.

> I just renamed some atomtypes and then added as the new atomtypes to .itp file, so I want to find a purposed atomtype and use its vdw parameter ( the same as what existed in .itp file.)

I'm not clear on the intent here.  You're creating duplicate atom types?  To what end?


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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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