[gmx-users] adding an acid as n-terminus
Velia Minicozzi
velia.minicozzi at roma2.infn.it
Thu Nov 13 11:45:53 CET 2014
Dear gmx-users,
we want to simulate a peptide which starts with an acidic terminus.
We used PRODRG to compute the coordinates and the FF for this new
residue and we followed all the gromacs instructions to insert a new
residue
(http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
Following the instructions, we inserted the new residue in the
gromos43a1ff rtp file and
we changed the hdb file accordingly.
Pdb2gmx give us the following error that we do not understand.
What else should we change?
We add to the email the pdbfile and the itp file computed by PRODRG
pdb2gmx -f provapept2.pdb -o provapept2.gro -p topol2.top -ignh -ter
.....
Fatal error:
Residue 2 named ACI of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
--
Velia Minicozzi
Universita' di Roma Tor Vergata
Dipartimento di Fisica
via della Ricerca Scientifica 1, I-00133 ROMA, Italy
Tel. +39.06.7259.4440 Fax +39.06.2023.507
Email: minicozzi at roma2.infn.it
-------------- next part --------------
;
;
; This file was generated by PRODRG version AA100323.0717
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 O 1 DRG OAA 1 -0.683 15.9994
2 C 1 DRG CAC 1 0.371 13.0190
3 C 1 DRG CAI 1 -0.018 12.0110
4 CR1 1 DRG CAG 1 -0.006 12.0110
5 HC 1 DRG HAG 1 0.027 1.0080
6 C 1 DRG CAH 1 -0.019 12.0110
7 BR 1 DRG IAB 1 0.307 126.9045
8 CR1 1 DRG CAE 1 -0.006 12.0110
9 HC 1 DRG HAE 1 0.027 1.0080
10 CR1 1 DRG CAD 2 -0.012 12.0110
11 HC 1 DRG HAD 2 0.012 1.0080
12 CR1 1 DRG CAF 3 -0.012 12.0110
13 HC 1 DRG HAF 3 0.012 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.123 16600000.0 0.123 16600000.0 ; CAC OAA
3 2 2 0.139 10800000.0 0.139 10800000.0 ; CAI CAC
3 4 2 0.139 10800000.0 0.139 10800000.0 ; CAI CAG
3 12 2 0.139 10800000.0 0.139 10800000.0 ; CAI CAF
4 5 2 0.109 12300000.0 0.109 12300000.0 ; CAG HAG
6 4 2 0.139 10800000.0 0.139 10800000.0 ; CAH CAG
6 7 2 0.209 2928800.0 0.209 2928800.0 ; CAH IAB
6 8 2 0.139 10800000.0 0.139 10800000.0 ; CAH CAE
8 9 2 0.109 12300000.0 0.109 12300000.0 ; CAE HAE
8 10 2 0.139 10800000.0 0.139 10800000.0 ; CAE CAD
10 11 2 0.109 12300000.0 0.109 12300000.0 ; CAD HAD
10 12 2 0.139 10800000.0 0.139 10800000.0 ; CAD CAF
12 13 2 0.109 12300000.0 0.109 12300000.0 ; CAF HAF
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; OAA CAG
1 12 1 ; OAA CAF
2 5 1 ; CAC HAG
2 6 1 ; CAC CAH
2 10 1 ; CAC CAD
2 13 1 ; CAC HAF
3 7 1 ; CAI IAB
3 8 1 ; CAI CAE
3 11 1 ; CAI HAD
4 9 1 ; CAG HAE
4 10 1 ; CAG CAD
4 13 1 ; CAG HAF
5 7 1 ; HAG IAB
5 8 1 ; HAG CAE
5 12 1 ; HAG CAF
6 11 1 ; CAH HAD
6 12 1 ; CAH CAF
7 9 1 ; IAB HAE
7 10 1 ; IAB CAD
8 13 1 ; CAE HAF
9 11 1 ; HAE HAD
9 12 1 ; HAE CAF
11 13 1 ; HAD HAF
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 121.0 685.0 121.0 685.0 ; OAA CAC CAI
2 3 4 2 120.0 560.0 120.0 560.0 ; CAC CAI CAG
2 3 12 2 120.0 560.0 120.0 560.0 ; CAC CAI CAF
4 3 12 2 120.0 560.0 120.0 560.0 ; CAG CAI CAF
3 4 5 2 120.0 505.0 120.0 505.0 ; CAI CAG HAG
3 4 6 2 120.0 505.0 120.0 505.0 ; CAI CAG CAH
5 4 6 2 120.0 505.0 120.0 505.0 ; HAG CAG CAH
4 6 7 2 120.0 560.0 120.0 560.0 ; CAG CAH IAB
4 6 8 2 120.0 560.0 120.0 560.0 ; CAG CAH CAE
7 6 8 2 120.0 560.0 120.0 560.0 ; IAB CAH CAE
6 8 9 2 120.0 505.0 120.0 505.0 ; CAH CAE HAE
6 8 10 2 120.0 505.0 120.0 505.0 ; CAH CAE CAD
9 8 10 2 120.0 505.0 120.0 505.0 ; HAE CAE CAD
8 10 11 2 120.0 505.0 120.0 505.0 ; CAE CAD HAD
8 10 12 2 120.0 505.0 120.0 505.0 ; CAE CAD CAF
11 10 12 2 120.0 505.0 120.0 505.0 ; HAD CAD CAF
3 12 10 2 120.0 505.0 120.0 505.0 ; CAI CAF CAD
3 12 13 2 120.0 505.0 120.0 505.0 ; CAI CAF HAF
10 12 13 2 120.0 505.0 120.0 505.0 ; CAD CAF HAF
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
3 2 12 4 2 0.0 167.4 0.0 167.4 ; imp CAI CAC CAF CAG
4 3 6 5 2 0.0 167.4 0.0 167.4 ; imp CAG CAI CAH HAG
6 8 7 4 2 0.0 167.4 0.0 167.4 ; imp CAH CAE IAB CAG
8 6 10 9 2 0.0 167.4 0.0 167.4 ; imp CAE CAH CAD HAE
10 8 12 11 2 0.0 167.4 0.0 167.4 ; imp CAD CAE CAF HAD
12 3 10 13 2 0.0 167.4 0.0 167.4 ; imp CAF CAI CAD HAF
3 4 6 8 2 0.0 209.3 0.0 209.3 ; imp CAI CAG CAH CAE
4 6 8 10 2 0.0 209.3 0.0 209.3 ; imp CAG CAH CAE CAD
6 8 10 12 2 0.0 209.3 0.0 209.3 ; imp CAH CAE CAD CAF
8 10 12 3 2 0.0 209.3 0.0 209.3 ; imp CAE CAD CAF CAI
10 12 3 4 2 0.0 209.3 0.0 209.3 ; imp CAD CAF CAI CAG
12 3 4 6 2 0.0 209.3 0.0 209.3 ; imp CAF CAI CAG CAH
12 3 2 1 1 180.0 5.9 2 180.0 5.9 2 ; dih CAF CAI CAC OAA
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