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. -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] > -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: [email protected] -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
