Esteban Gabriel Vega Hissi wrote:
Justin,
Regarding the charges you mention, what do you think about RESP charges
for this kind of compounds (drugs) parameterization?
We have not found any single charge calculation method that correctly reproduces
the charges on Gromos96 charge groups, so further iterative refinement and
validation is a must. We recommend AM1-BCC for an initial charge calculation,
as it actually produces charges that are consistently more comparable to those
expected in the force field.
The groups in Gromos96 are very transferable across molecules, so piecing
together a novel molecule from building blocks works quite well. It's only for
those unknown groups that you'd have to derive new charges.
As soon as our paper is out, I will link it from the Parameterization and PRODRG
pages on the wiki, since this is a very common question.
-Justin
Best wishes
Esteban
--
On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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>
<mailto: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> <mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
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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