[gmx-users] Re: Using new atom types
fabian.casteblanco at gmail.com
Thu Jul 7 22:49:17 CEST 2011
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
don't think I have access to change internal files. I do not need to
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?
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
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E: fabian.casteblanco at gmail.com
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