[gmx-users] free energy perturbation

Hello, I am doing free energy perturbation for ethane to methanol conversion. Can anybody tell me which of the following way is right to define virtual site for hydrogen? [ virtual_sites2 ] 3 2 1 1 0.00 or [ virtual_sites2 ] 3 2 1 1 1.00 Thanking you in anticipation. With regards,

[gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)

Dear Justin I got the solution. I forgot to add residue types in residuetypes.dat Anyway thanks for your kind reply with regards, Jignesh Patel On Mon, Nov 29, 2010 at 12:17 PM, Jignesh Patel jbp...@gmail.com wrote: Dear Justin, Thanks for your reply. I have checked whole pdb file

[gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)

://www.gromacs.org/Documentation/Errors --- Thanking you. With regards, Jignesh Patel On Sat, Nov 27, 2010 at 4:30 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe

[gmx-users] Error while using forcefield GROMOS 43a1p

. With regards, Jignesh Patel -- gmx-users mailing listgmx-users@gromacs.org 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

[gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

Dear all, Can anybody tell me how to incorporate potassium ion parameters in GROMACS for GROMOS53a6 forcefield. Thanking you in anticipation. With regards, Jignesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] Cutoff value during lipid shrinking using inflategro.pl script

DPPC * 0 * system_shrink1.gro 5 area_shrink1.dat Thanking You in anticipation. -- Best Wishes, Jignesh Patel M.S.(Pharm.), Center for Pharmacoinformatics, NIPER, S.A.S. Nagar, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] How to remove overlapping lipid residues?

Hello, Can anyone tell me how to remove overlapping lipid residues? Thanking you. -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] Regarding Error Atomtype OS not found

code file: toppush.c, line: 947 Fatal error: Atomtype OS not found Can anyone help me to solve this problem? Any kind of help is highly appreciable. -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Regarding inflategro.pl

Dear Justin, When I used inflategro.pl, it removed original water molecules of DPPC128 membrane. After that i added water using genbox. Is it correct method to follow? Thanking you in anticipation. -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- gmx-users mailing listgmx