On 4/8/14, 12:45 PM, Chris Ing wrote:
I'm trying to build a charmm36.ff topology file for a POPC with virtual sites. In GROMACS 4.5.5 and 4.6.3 (with the most recent CHARMM36 March 2014), when I run: pdb2gmx -f POPC.pdb -o POPC.gro -p POPC.top -i POPC.posre -vsite hydrogen grompp -f empty.mdp -c POPC.gro -p POPC.top -o test.tpr I get multiple constraint errors: ERROR 1 [file POPC.top, line 311]: No default Constr. No Conn. types Which is due to the lack of two constraints not in ffbonded.itp: MCH3 NTL MCH3 CTL2 MCH3 is the virtual site of a CH3 group, and NTL refers to the choline nitrogen in the POPC headgroup and CTL2, in this case, is the carbon closest to the CH3 group on the POPC tail. The same question was asked in the gmx-users thread "amber99sb_virtual site lipids dopc MCH3_N constraint types" by Song Ke, where the reply from Erik Marklund was to manually add this value "from bond lengths, center of mass for the group and the moment of inertia.". In lieu of wiping an inch of dust off my classical mechanics textbook, I wondered if I could copy some additional constraint values from the OPLS ffbonded.itp file. The charmm36.ff ffbonded.itp file states that the constrainttypes section is copied directly from OPLS (the restraint values are slightly adjusted?). Yet, many entries were not copied from OPLS to CHARMM36: OPLS: MNH3 CT_2 2 0.158255 MNH3 MNH3 2 0.080236 MCH3A C 2 0.166040 MCH3A C_2 2 0.166040 MCH3A CW 2 0.164312 MCH3A CV 2 0.164312 MCH3A CS 2 0.163448 MCH3A CA 2 0.164888 MCH3A CB 2 0.164888 MCH3A N 2 0.159040 MCH3A S 2 0.193874 MCH3A MCH3A 2 0.092160 MCH3B CT 2 0.167031 MCH3B CT_2 2 0.167031 MCH3B CT_3 2 0.167031 MCH3B CO 2 0.167031 MCH3B MCH3B 2 0.091456 CHARMM36: MNH3 CT3 2 0.159603 MNH3 MNH3 2 0.082619 MCH3 CT1 2 0.168122 MCH3 CT2 2 0.167162 MCH3 CT3 2 0.167354 MCH3 S 2 0.195314 MCH3 MCH3 2 0.093582 Would it be acceptable to use these OPLS constraint values in CHARMM36 to resolve my problem?: MCH3A N 2 0.159040 MCH3B CT 2 0.167031 Thanks gmx-users/Justin Lemkul!
For what it's worth, we have done exactly zero testing with virtual sites. The sections of text you are referring to were copied basically verbatim from what was distributed as charmm27.ff in Gromacs prior to our creation of charmm36.ff. I don't know if that's of any use, but please consider it at least a strong disclaimer :)
-Chris P.S. I had similar missing dihedral/ub errors when trying to build my charmm36.ff protein topology with virtual sites whenever I used a neutral terminus. I didn't look into the details because using a charged terminus, I had no errors.
If you can provide me with specific errors and the atomtypes to which they correspond, I will look into it. We recently fixed a problem with missing U-B types for neutral termini with branched-chain amino acids, but the necessary parameters were added before our March release. To my knowledge, that issue should be resolved, but if there are remaining problems, I'd be happy to look into it. If it only occurs when using virtual sites, again, that's because we never looked into it.
-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.
