Please don't reply to the entire digest. If you want to ask a new question, just send a new message to the mailing list.
On 2/9/16 5:34 AM, Mehreen Jan wrote:
gromacs4.5.5 phosphorylated protein - protein-protein interaction phosphate at "SEP" and TPO forcefield 43A1p download from gromacs web page command: pdb2gmx -f protein.pdb -p protein.top -o protein.gro fatal error: error in hdb file ./gromos43A1p.ff/aminoacid.hdb wrong number of control atoms (2 iso 3) on line: 2 3 N -C -CA i read manual but i can't remove error. i did not get the point how to remove error HDB file s given:
There is no line in this file that would trigger that error. Make sure you're looking at, and trying to use, the right files.
-Justin
ABU 1 1 1 H N -C CA ACEH 1 3 4 HA CA C O AIB 1 1 1 H N -C CA ALA 1 1 1 H N -C CA ARG 4 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH1 NH1 CZ NE 2 3 HH2 NH2 CZ NE ARGN 4 1 1 H N -C CA 1 1 HE NE CD CZ 1 2 HH1 NH1 CZ NE 2 3 HH2 NH2 CZ NE ASN 2 1 1 H N -C CA 2 3 HD2 ND2 CG CB ASP 1 1 1 H N -C CA ASP1 2 1 1 H N -C CA 1 2 HD1 OD1 CG CB ASPH 2 1 1 H N -C CA 1 2 HD2 OD2 CG CB BEN 7 1 1 H2 C2 C1 C3 1 1 H3 C3 C2 C4 1 1 H4 C4 C3 C5 1 1 H5 C5 C4 C6 1 1 H6 C6 C5 C1 2 3 H1 N1 C7 C1 2 3 H2 N2 C7 C1 CYS2 1 1 1 H N -C CA CYSH 2 1 1 H N -C CA 1 2 HG SG CB CA FAD 7 2 3 HN6 AN6 AC6 AC5 1 2 HO2* AO2* AC2* AC1* 1 2 HO3* AO3* AC3* AC2* 1 2 H4* O4* C4* C5* 1 2 H3* O3* C3* C4* 1 2 H2* O2* C2* C3* 1 2 H3 N3 C4 C4A GLN 2 1 1 H N -C CA 2 3 HE2 NE2 CD CG GLU 1 1 1 H N -C CA GLUH 2 1 1 H N -C CA 1 2 HE2 OE2 CD CG GLY 1 1 1 H N -C CA HEME 4 1 1 HHA CHA C1A C4D 1 1 HHB CHB C1B C4A 1 1 HHC CHC C1C C4B 1 1 HHD CHD C1D C4C HIS1 2 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 HISA 2 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 HISB 2 1 1 H N -C CA 1 1 HE2 NE2 CE1 CD2 HISH 3 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 1 1 HE2 NE2 CE1 CD2 HO4 1 3 10 HW OW HOH 1 2 7 HW OW HYP 1 1 2 HD1 OD1 CG CB ILE 1 1 1 H N -C CA LEU 1 1 1 H N -C CA LYS 2 1 1 H N -C CA 2 4 HZ NZ CE CD LYSH 2 1 1 H N -C CA 3 4 HZ NZ CE CD MET 1 1 1 H N -C CA NAC 1 1 1 H N -C CA NACH 2 1 1 H N -C CA 3 4 HA CA N NH NH2 1 2 3 H N -C -CA PHE 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 1 HZ CZ CE1 CE2 PHEU 1 1 1 H N -C CA PHL 7 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 1 HZ CZ CE1 CE2 1 2 HY OY CX CA SER 2 1 1 H N -C CA 1 2 HG OG CB CA TFE 1 1 2 H O CH2 C THR 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA TRP 7 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 1 HZ3 CZ3 CE3 CH2 1 1 HH2 CH2 CZ3 CZ2 1 1 HZ2 CZ2 CE2 CH2 TRPU 2 1 1 H N -C CA 1 1 HE1 NE1 CD1 CE2 TYR 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 2 HH OH CZ CE1 TYRU 2 1 1 H N -C CA 1 2 HH OH CZ CE1 VAL 1 1 1 H N -C CA SEP 1 1 1 H N -C CA TPO 1 1 1 H N -C CA PTR 5 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ SEPH 2 1 1 H N -C CA 1 2 H3P O3P P OG TPOH 2 1 1 H N -C CA 1 2 H3P O3P P OG1 PTRH 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 2 H3P O3P P OH thank you mehreen
-- ================================================== 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 [email protected] | (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 [email protected].
