[gmx-users] C-terminus residue name in Gromos43a1
fra
francesca.vitalini11 at gmail.com
Thu Feb 27 15:51:49 CET 2014
I am using Gromacs 4.5.5. In my residuetypes.dat ACE is correctly listed as
protein residue and pdb2gmx doesn't give any error about protein type.
For clarity I copy here my pdb, the interesting parts of the aminoacids.rtp
file and the pdb2gmx command.
Thank you very much for any help you can give.
#####################################
FROM aminoacids.rtp
#####################################
[ ACE ]
[ atoms ]
CA CH3 0.000 0
C C 0.380 1
O O -0.380 1
[ bonds ]
C CA gb_26
C O gb_4
C +N gb_9
[ angles ]
CA C O ga_30
CA C +N ga_18
O C +N ga_32
[ impropers ]
C CA +N O gi_1
[ ALA ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH3 0.00000 1
C C 0.380 2
O O -0.380 2
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
[ NAC ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH3 0.00000 0
[ bonds ]
N CA gb_20
N H gb_2
-C N gb_9
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
#####################################
pdb file
#####################################
TER
#####################################
pdb2gmx
#####################################
pdb2gmx -f Ac_A_NHMe/Ac_A_NHMe_gromos.pdb -o Ac_A_NHMe/Ac_A_NHMe.gro -p
Ac_A_NHMe/Ac_A_NHMe.top -i Ac_A_NHMe/Ac_A_NHMe.itp -n
Ac_A_NHMe/Ac_A_NHMe.ndx -q Ac_A_NHMe/Ac_A_NHMe.pdb -ignh -ter
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) pdb2gmx (-:
Option Filename Type Description
------------------------------------------------------------
-f Ac_A_NHMe/Ac_A_NHMe_gromos.pdb Input Structure file: gro g96
pdb
Reading Ac_A_NHMe/Ac_A_NHMe_gromos.pdb...
Read 'ACETYL-ALANINE-METHYLAMIDE', 10 atoms
Back Off! I just backed up Ac_A_NHMe/Ac_A_NHMe.pdb to
Ac_A_NHMe/#Ac_A_NHMe.pdb.5#
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 0 residues with 10 atoms
chain #res #atoms
1 'A' 1 1
2 ' ' 3 9
All occupancies are one
Opening force field file ./gromos43a1_modifiedwithNAC.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos43a1_modifiedwithNAC)
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.rtp
Residue 97
Sorting it all out...
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.hdb
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.n.tdb
Opening force field file ./gromos43a1_modifiedwithNAC.ff/aminoacids.c.tdb
Back Off! I just backed up Ac_A_NHMe/Ac_A_NHMe.top to
Ac_A_NHMe/#Ac_A_NHMe.top.5#
Processing chain 1 'A' (1 atoms, 1 residues)
Identified residue ACE1 as a starting terminus.
Identified residue ACE1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ACE-1
0: NH3+
1: NH2
2: None
2
Start terminus ACE-1: None
Select end terminus type for ACE-1
0: COO-
1: COOH
2: None
2
End terminus ACE-1: None
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1034
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a
proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Francesca
--
View this message in context: http://gromacs.5086.x6.nabble.com/C-terminus-residue-name-in-Gromos43a1-tp5014776p5014844.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
More information about the gromacs.org_gmx-users
mailing list