[gmx-users] Re: Using new atom types

Fabian Casteblanco fabian.casteblanco at gmail.com
Thu Jul 7 23:32:24 CEST 2011

Hello Justin,

Thanks for your help.

Your response:
No, you need the [defaults] directive from the force field.  If you
want to make
a completely custom entity, then build your own, although likely most of the
highest-level force field files are going to be the same.  You can always add a
new [atomtypes] directive in a proper location in your topology.

Comment:  So you are saying I need to refer to the [defaults]
directive so I need to include {#include "charmm27.ff/forcefield.itp"}
on my topology file?  Below is the [defaults] directive for CHARMM.  I
can simply add my...

>> -CgenFFbon.itp   (bonded, angle, dihedral parameters,etc)
>> -CgenFFnb.itp     (nonbonded LJ values)
>> -CgenFF.atp        (atom type file)

to this section?

*               Charmm to Gromacs port writted by              *
*               Par Bjelkmar, bjelkmar at cbr.su.se               *
*               Alternative correspondance:                    *
*               Erik Lindahl, lindahl at cbr.su.se                *

#define _FF_CHARMM

[ defaults ]
; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
1	2	yes	1.0	1.0

#include "ffcharmm27nb.itp"
#include "ffcharmm27bon.itp"
**???{  #include add new CgenFFbon.itp and CgenFFnb.itp here? }???**    ?

Or would I need to create one almost identical to this except
replacing the old ffcharm27.itp with my new Cgen.itp files?

This is my sample topology.  Your last statement said I could add
[atomtypes] to this section.  So I can simply include the [defaults]
directive but just add the Cgenffbon.itp and cCgenffnb.itp to this
section here?

;SAMPLE topology:
; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
**???{  #include add new CgenFFbon.itp and CgenFFnb.itp here? }???**    ?

#include "drug.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
DDD                      1

Thanks again for your help.  Greatly appreciated!!

Fabian Casteblanco
Rutgers University

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