On 3/11/14, 6:32 AM, Nidhi Katyal wrote:
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well as [molecule] entry. I have followed the following procedure to #include while creating my first molecule: Run pdb2gmx command. Added #include "ligand.itp" after #include "charmm27.ff/forcefield.itp" but before [ moleculetype ] ; Name nrexcl Protein_chain_A 3 and added at the end: [ molecules ] ; Compound #mols Protein_chain_A 1 LIG 1 SOL 17063 then I have merged protein and ligand coordinates by inserting ATOM lines from ligand.pdb to *.pdb generated after pdb2gmx command. Then. I run editconf, genbox and finally grompp command. After which I got following error: Fatal error: No such moleculetype LIG My both *.itp and *.pdb files contains LIG. How to rectify the error? Thanks in advance.
Residue name and [moleculetype] name are not necessarily equivalent. You'll have to post the actual content of lig.itp to get any real useful diagnostic feedback.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
