Just the $0.02 that I always seem to contribute in these types of discussions -
the topology you have shown below contains some likely problems. The charges
(and massive charge group size) can lead to artifacts. We've got a paper due
out soon about the implications of incorrect charges, but I would advise you
that this topology should *not* be used for production simulation. You'd be
better off spending the time to properly parameterize the molecule rather than
run a bunch of simulations and get questionable (at best) or wrong (at worst)
results.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
Olga Ivchenko wrote:
Hey Vitaly,
Thank you for your reply. Here is the files:
*itp:*
;
;
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to d...@davapc1.bioch.dundee.ac.uk
<mailto:d...@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 OM 1 DRG OXT 1 -0.701 15.9994
2 C 1 DRG C 1 0.402 12.0110
3 OM 1 DRG O 1 -0.701 15.9994
4 CH2 1 DRG CA 2 0.185 14.0270
5 N 1 DRG N 2 0.468 14.0067
6 CH3 1 DRG CAG 2 0.201 15.0350
7 C 1 DRG CAH 2 0.377 12.0110
8 NZ 1 DRG NAE 2 -0.163 14.0067
9 H 1 DRG HA6 2 0.023 1.0080
10 H 1 DRG HAE 2 0.024 1.0080
11 NZ 1 DRG NAD 2 -0.163 14.0067
12 H 1 DRG HA5 2 0.024 1.0080
13 H 1 DRG HAD 2 0.024 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.125 13400000.0 0.125 13400000.0 ; C OXT
2 3 2 0.125 13400000.0 0.125 13400000.0 ; C O
2 4 2 0.153 7150000.0 0.153 7150000.0 ; C CA
5 4 2 0.147 8710000.0 0.147 8710000.0 ; N CA
5 6 2 0.147 8710000.0 0.147 8710000.0 ; N CAG
5 7 2 0.134 10500000.0 0.134 10500000.0 ; N CAH
7 8 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAE
7 11 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAD
8 9 2 0.100 18700000.0 0.100 18700000.0 ; NAE HA6
8 10 2 0.100 18700000.0 0.100 18700000.0 ; NAE HAE
11 12 2 0.100 18700000.0 0.100 18700000.0 ; NAD HA5
11 13 2 0.100 18700000.0 0.100 18700000.0 ; NAD HAD
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; OXT N
2 6 1 ; C CAG
2 7 1 ; C CAH
3 5 1 ; O N
4 8 1 ; CA NAE
4 11 1 ; CA NAD
5 9 1 ; N HA6
5 10 1 ; N HAE
5 12 1 ; N HA5
5 13 1 ; N HAD
6 8 1 ; CAG NAE
6 11 1 ; CAG NAD
8 12 1 ; NAE HA5
8 13 1 ; NAE HAD
9 11 1 ; HA6 NAD
10 11 1 ; HAE NAD
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 126.0 770.0 126.0 770.0 ; OXT
C O
1 2 4 2 117.0 635.0 117.0 635.0 ; OXT
C CA
3 2 4 2 117.0 635.0 117.0 635.0 ; O
C CA
2 4 5 2 109.5 520.0 109.5 520.0 ; C
CA N
4 5 6 2 121.0 685.0 121.0 685.0 ; CA N
CAG
4 5 7 2 122.0 700.0 122.0 700.0 ; CA N
CAH
6 5 7 2 117.0 635.0 117.0 635.0 ; CAG N
CAH
5 7 8 2 120.0 670.0 120.0 670.0 ; N CAH
NAE
5 7 11 2 120.0 670.0 120.0 670.0 ; N CAH
NAD
8 7 11 2 120.0 670.0 120.0 670.0 ; NAE CAH
NAD
7 8 9 2 120.0 390.0 120.0 390.0 ; CAH NAE
HA6
7 8 10 2 120.0 390.0 120.0 390.0 ; CAH NAE
HAE
9 8 10 2 120.0 445.0 120.0 445.0 ; HA6 NAE
HAE
7 11 12 2 120.0 390.0 120.0 390.0 ; CAH NAD
HA5
7 11 13 2 120.0 390.0 120.0 390.0 ; CAH NAD
HAD
12 11 13 2 120.0 445.0 120.0 445.0 ; HA5 NAD
HAD
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp C
OXT O CA
5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp N
CA CAG CAH
7 5 8 11 2 0.0 167.4 0.0 167.4 ; imp CAH
N NAE NAD
8 7 10 9 2 0.0 167.4 0.0 167.4 ; imp NAE
CAH HAE HA6
11 7 13 12 2 0.0 167.4 0.0 167.4 ; imp NAD
CAH HAD HA5
5 4 2 1 1 0.0 1.0 6 0.0 1.0 6 ; dih N
CA C OXT
2 4 5 7 1 180.0 1.0 6 180.0 1.0 6 ; dih C
CA N CAH
11 7 5 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD
CAH N CA
5 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N
CAH NAE HAE
5 7 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih N
CAH NAD HAD
*And top. I am prettu sure this file is wrong. And I do not know yet how
to modify it correctly:
*
;
; File 'creatine.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Mon Nov 15 13:24:44 2010
;
; This is your topology file
; it was generated using program:
; pdb2gmx - version 4.5-beta2
; with command line:
; pdb2gmx -f creatine_all_hyd_PRODRGBeta.pdb -o creatine.gro -p
creatine.top
;
#include "creatine.itp"
#include "gromos43a1.ff"
; Include forcefield parameters
;#include "gromos43a1.ff/forcefield.itp"
;"gromos43a1.ff/creatine.itp"
;[ system ]
;[ molecules ]
;DRG 3
2010/11/15 Vitaly Chaban <vvcha...@gmail.com <mailto:vvcha...@gmail.com>>
Hey, Olga -
> Also please can you tell me where can I get "ffgmx.itp" file?
/$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other
standard topology files are there.
By trying to run md I am getting an error: Fatal error:
> moleculetype UNK is redefined
Please post you top and itp files here. Looks like you have 2 creatine
molecules in your topology right now.
Good luck!
Vitaly
> I still have troubles of starting running md for creatine. For
which I
> created topology using PRODRG programm.
> The only difference between creatine.top and creating.itp is that
creatine
> top has additional lines:
> #include "ffgmx.itp"
> #include "creatine.itp"
>
> Also please can you tell me where can I get "ffgmx.itp" file?
>
> By trying to run md I am getting an error: Fatal error:
> moleculetype UNK is redefined
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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