[gmx-users] wrong number of control atoms (2 iso 3) on line: 2 3 N -C -CA
Justin Lemkul
jalemkul at vt.edu
Wed Feb 10 03:24:18 CET 2016
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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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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