On 2/3/14, 10:14 PM, Sidath Wijesinghe wrote:
Justin,, i rechecked the opls/ff that i used and found some errors, after correction them i got the .top file. note that i was able to define the charge groups as well. when i use this .top file with grompp, now am getting 12 errors...as follwos.. ERROR 1 [file topol.top, line 1399]: No default Ryckaert-Bell. types ERROR 2 [file topol.top, line 1400]: No default Ryckaert-Bell. types ERROR 3 [file topol.top, line 1415]: No default Ryckaert-Bell. types ERROR 4 [file topol.top, line 1416]: No default Ryckaert-Bell. types and so on... i did the mapping as you suggested,as an example line 1399 in .top as follwos... 2 1 82 81 3 ( here 2 1 82 & 81 are carbon atoms) and the mapping to all 12 errors.....then modified the ffbonded.itp file's diheadral block as follows... C2 C1 C82 C81 3 0.00 0.00 0.00 0.00 so on.... then bond tyype block as follows.... C2 C1 1 0.00 0.00... so on.... added those atom types in atomtypes.atp like below... C1 C2 C3 C4 C11 C12 C13................so on after that when i do grompp gives me a fatal error like Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 631 Fatal error: Unknown bond_atomtype C1 could you please tell me what i have done wrong?
You used atom names, not atom types. In [atoms] in your .top, each atom type is assigned as opls_XXX. Looking in ffnonbonded.itp, the second column of the corresponding opls_XXX type is its bonded type equivalent. That is the identifier you need to be using. The force field doesn't care what atoms are named, but it does care what type they are.
and at the same time....i tied delete those 12 lines in .top and do grompp...it worked....but when i did mdrun.....i am getting the signs of blowing up system....what i can do over here....how can i get rid of these errors and carry out my simulation?
Of course if you delete an essential bonded interaction, the simulation will go haywire. Deletion may be convenient for getting grompp to shut up, but it's not sound practice.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. 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.
