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, [email protected] *
* Alternative correspondance: *
* Erik Lindahl, [email protected] *
****************************************************************
#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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