On 6/22/17 11:23 AM, Dilip H N wrote:
No, its not related to parameterization methodology. it is a different question... how can i identify the molecule as methylamine (for example) since in the .rtp the molecule type is written as [MAM1] [ MAM1 ] [ atoms ] N1 NG321 -0.990 0 C1 CG3AM2 -0.060 1 HN1 HGPAM2 0.390 2 HN2 HGPAM2 0.390 3 HC1 HGAAM2 0.090 4 HC2 HGAAM2 0.090 5 HC3 HGAAM2 0.090 6 [ bonds ] N1 C1 N1 HN1 N1 HN2 C1 HC1 C1 HC2 C1 HC3 Is thr any hint such tht i can identify the molecule type written in .rtp file.?? Or should i manually find it out..??... but in case of Glycine the molecule type is [GLY] which is easy to find.... How can i solve this issue..??
You need to go to the original CHARMM force field files. These include names and (typically) chemical structure drawings.
http://mackerell.umaryland.edu/charmm_ff.shtml#charmm -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.