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.
-Justin
Thanks for you help.
-Fabian
On Thu, Jul 7, 2011 at 2:16 PM, Fabian Casteblanco
<[email protected]> 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: [email protected]
--
========================================
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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