[gmx-users] Re: Using new atom types

[Justin A. Lemkul]

Fabian Casteblanco wrote:
> 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? }???**    ?
> 

No, because the required directives would be out of order and grompp would fail 
with a fatal error.

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

That depends.  If your CgenFF* files are completely independent of the CHARMM27 
force field files already built into Gromacs, then yes, you can build everything 
from scratch.  If you need any of the parameters from the existing CHARMM27 
force field, then you have to include your new parameters.

> 
> 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? }???**    ?
> 

No, this would have the same effect as above.  What is weird here is that this 
.top uses version 4.5 naming, but the files above appear to be from the 4.0.x 
series.  Mixing these will probably not work.  Be sure to standardize the files 
you're using to be consistent with the expectations of the Gromacs version 
you're using.

The bottom line is that you should have a thorough read of Chapter 5 of the 
manual to understand the contents of the topology, from the highest level (force 
field) down to the molecule level, in terms of both the required order of 
directives and contents thereof.  If the CGenFF parameters do not depend on the 
existing implementation, then you're probably better off not messing with the 
existing files and just creating your own, styled after the existing force field.

-Justin

> #include "drug.itp"
> 
> [ system ]
> ; Name
> DrugName
> 
> [ molecules ]
> ; Compound        #mols
> DDD                      1
> 
> 
> 
> Thanks again for your help.  Greatly appreciated!!
> 
> Fabian Casteblanco
> Rutgers University

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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