[gmx-users] Re: Using new atom types

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 7 23:07:14 CEST 2011

Fabian Casteblanco wrote:
> Hello Peter C. Lai,
> Thanks for your help.  I read your back and forth posts on the GMX
> Forums with Mark Abraham.  Is there any way that I can simply use it
> from the topology without having to include it on the
> charmm27.ff/forcefield.itp?  I have to run this on a cluster and I

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.

> don't think I have access to change internal files.  I do not need to

Then make a local copy of anything you need to change.  grompp, etc search the 
working directory before $GMXLIB.

> run using pdb2gmx.  Also, how did you manage to include the LJ 1-4
> parameters?  Did you have to write out each and every pair on GROMACS?

The CHARMM force field has gen-pairs (in forcefield.itp) set to yes, so any 
[pairtype] that is not found will be generated.


> Thanks for you help.
> -Fabian
> On Thu, Jul 7, 2011 at 2:16 PM, Fabian Casteblanco
> <fabian.casteblanco at gmail.com> wrote:
>> Hello all,
>> I'm building a drug molecule using CHARMM parameters.  The thing is
>> that there is this new CGenFF (an extension of CHARMM, but very
>> similar to the old CHARMM atom types
>> http://mackerell.umaryland.edu/~kenno/cgenff/) that uses better
>> parameters for drug-like molecules.  I would like to use these new
>> parameters for this drug molecule (pretty big molecule).  I took all
>> the parameter values from CGenFF and I converted them to values used
>> by Gromacs and I formatted it just like the original ffcharm27.itp
>> files found in Gromacs.  The only thing is that when it comes to
>> Lennard Jones,1-4 parameters, CHARMM gives you the actual individual
>> value by atom whereas Gromacs has already all the pair listed values
>> stored.  Is there any way that I can place these 1-4 parameters in the
>> drug.itp file itself and have Gromacs calculate the combinations just
>> as it does for the regular LJ values?
>> I have:
>> -CgenFFbon.itp   (bonded, angle, dihedral parameters,etc)
>> -CgenFFnb.itp     (nonbonded LJ values)
>> -CgenFF.atp        (atom type file)
>> What exactly do I need to include on my drug.itp (or drug.top) file
>> inorder so it can read these parameters from the files above?
>> Thanks for anyones help!  Greatly appreciated!!
>> ;SAMPLE topology:
>> ;
>> ;
>> ; Include forcefield parameters
>> #include "charmm27.ff/forcefield.itp"
>> #include "drug.itp"
>> [ system ]
>> ; Name
>> DrugName
>> [ molecules ]
>> ; Compound        #mols
>> DDD                    1
>> --
>> Best regards,
>> Fabian F. Casteblanco
>> Rutgers University --
>> Chemical Engineering PhD Student
>> C: +908 917 0723
>> E:  fabian.casteblanco at gmail.com


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


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