Oliver Grant wrote:
The force fields have to be compatible but this way works fine.
I guess that depends on what you mean by "works fine." If you mean that you can
produce a stable simulation, then yes, it may "work," but I would question the
underlying premise of combining different force fields. If, for example, you're
using an AMBER force field for, say, a protein, and OPLS for a small molecule,
then what you're doing is wrong. The combination rules required by both force
fields are different, as are the underlying derivation schemes and quite
possibly some more details I'm not thinking about at the moment.
I guess it all depends on what you mean (below) by "non amber force field" and
how different it is from the actual requirements of the AMBER force field you're
using. If this "non amber force field" was designed to be compatible with your
chosen force field, and there was some suitable derivation scheme involved, then
things will probably work. If you're mixing and matching parameter sets, be
prepared for very tough questions from any reviewers who see your work.
-Justin
On 19 May 2010 12:50, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Oliver Grant wrote:
Can you not run pdb2gmx for each of your molecules that you want
separate force fields for? Then cat the gro files, renumber and
include the molecule types as .itp files in the .top file as
below. If I'm doing anything wrong please let me know! :)
Combining different force fields into a single system completely
invalidates it, so yes, I'd say you're doing something wrong :)
-Justin
;
; This is your topology file
; "What If None Of Your Dreams Come True ?" (E. Costello)
;
; Include forcefield parameters
#include "ffamber99sb.itp"
[ atomtypes ]
------------------------------------------------------------------------------------from
the top file of the non amber force field
;name bond_type mass charge ptype sigma
epsilon
CY CY 0.0000 0.0000 A 3.39967e-01 4.57730e-01
O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01
HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00
H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02
O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01
N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01
H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02
OY OY 0.0000 0.0000 A 3.00001e-01 7.11280e-01
HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02
H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02
C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01
OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01
CG CG 0.0000 0.0000 A 3.39967e-01 4.57730e-01
OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01
#include
"protein.itp"------------------------------------------------------------------------------------from
the top file of the amber force field, contains everything
usually specified here under [molecule types].
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
#ifdef POSRES_CA
#include "CA_posre.itp"
#endif
#include
"trisacc.itp"------------------------------------------------------------------------------------from
the top file of the non amber force field, contains charges etc.
; Include Position restraint file
#ifdef POSRES_trisacc
#include "trisacc_posre.itp"
#endif
; Include water topology
#include "ffamber_tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "Na_amber99sb.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_A 1
trisacc 1
SOL 10697
Na 4
2010/5/19 you zou <zou....@live.com <mailto:zou....@live.com>
<mailto:zou....@live.com <mailto:zou....@live.com>>>
Hi Justin,
Thank you for your help, But when I run x2top command there
is one
error that is:
"
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207
Fatal error:
Could only find a forcefield type for 6 out of 24 atoms"
I don't know how can I adjust this error.
I have one more question again, this command give me a top
file, if
I want gro file of this pdb (drug that has removed from
drug-enzyme
complex) how can I do that?
you zou wrote:
> Dear Users,
> > I have one question about Drug-Enzyme Complex,Similar
to tutorial If I
>
want to use GROMOS96 43a1, I can use "Prodrg Beta version"
for drug > but If I want to use OPLS-AA/L all-atom force
field I can use "Prodrg > Beta version" server too, or not?
No. You can't use two different force fields in one
simulation system.
> If I can't use this server, how can I make .gro file and
.itp file for > drug that remove from initial .pdb file?
>
There are several programs in the User Contributions from the
website, x2top
(which is distributed with Gromacs), or you can build the
topology by hand. No matter what you choose, you need a
thorough understanding of the mechanics of your chosen force
field, methods of validation, and of course Chapter 5 in the
Gromacs manual.
Thanks
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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 <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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