[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.
> 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
>> [ 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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