<br>
<i>I guess that depends on what you mean by "works fine." </i><br><br>I mean the method of using pdb2gmx to generate a top and gro and then appending the gro files and including the .itp files in the .top file, works if you want to use two force fields. Originally I thought that was the question.<br>
<br>
<i>I guess it all depends on what you mean (below) by "non amber force
field"</i><br><br>I'm using GLYCAM06, so it involves a bit more effort to generate a .top and .gro file than just using pdb2gmx but I thought I'd leave it out as I just wanted to explain the method I use to include it. Apologies for the confusion!<br>
<br>Oliver<br><br><br>
<br>
-Justin<br><br><div class="gmail_quote">On 20 May 2010 13:00, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
Oliver Grant wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
The force fields have to be compatible but this way works fine.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
On 19 May 2010 12:50, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Oliver Grant wrote:<br>
<br>
Can you not run pdb2gmx for each of your molecules that you want<br>
separate force fields for? Then cat the gro files, renumber and<br>
include the molecule types as .itp files in the .top file as<br>
below. If I'm doing anything wrong please let me know! :)<br>
<br>
<br>
Combining different force fields into a single system completely<br>
invalidates it, so yes, I'd say you're doing something wrong :)<br>
<br>
-Justin<br>
<br>
<br>
;<br>
; This is your topology file<br>
<br>
; "What If None Of Your Dreams Come True ?" (E. Costello)<br>
;<br>
; Include forcefield parameters<br>
#include "ffamber99sb.itp"<br>
<br>
[ atomtypes ]<br>
------------------------------------------------------------------------------------from<br>
the top file of the non amber force field<br>
;name bond_type mass charge ptype sigma epsilon<br>
CY CY 0.0000 0.0000 A 3.39967e-01 4.57730e-01<br>
O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01<br>
HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00<br>
H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02<br>
O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01<br>
N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01<br>
H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02<br>
OY OY 0.0000 0.0000 A 3.00001e-01 7.11280e-01<br>
HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02<br>
H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02<br>
C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>
OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01<br>
CG CG 0.0000 0.0000 A 3.39967e-01 4.57730e-01<br>
OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01<br>
<br>
#include<br>
"protein.itp"------------------------------------------------------------------------------------from<br>
the top file of the amber force field, contains everything<br>
usually specified here under [molecule types].<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
<br>
#ifdef POSRES_CA<br>
#include "CA_posre.itp"<br>
#endif<br>
<br>
#include<br>
"trisacc.itp"------------------------------------------------------------------------------------from<br>
the top file of the non amber force field, contains charges etc.<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_trisacc<br>
#include "trisacc_posre.itp"<br>
#endif<br>
<br>
; Include water topology<br>
#include "ffamber_tip3p.itp"<br>
<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
; Include generic topology for ions<br>
#include "Na_amber99sb.itp"<br>
<br>
[ system ]<br>
; Name<br>
Protein in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
trisacc 1<br>
SOL 10697<br>
Na 4<br>
<br>
<br>
<br>
2010/5/19 you zou <<a href="mailto:zou.you@live.com" target="_blank">zou.you@live.com</a> <mailto:<a href="mailto:zou.you@live.com" target="_blank">zou.you@live.com</a>><br></div></div>
<mailto:<a href="mailto:zou.you@live.com" target="_blank">zou.you@live.com</a> <mailto:<a href="mailto:zou.you@live.com" target="_blank">zou.you@live.com</a>>>><div><div></div><div class="h5"><br>
<br>
<br>
Hi Justin,<br>
<br>
Thank you for your help, But when I run x2top command there<br>
is one<br>
error that is:<br>
"<br>
Can not find forcefield for atom C1-1 with 2 bonds<br>
Can not find forcefield for atom C4-4 with 2 bonds<br>
...<br>
Program x2top, VERSION 4.0.5<br>
Source code file: x2top.c, line: 207<br>
<br>
Fatal error:<br>
Could only find a forcefield type for 6 out of 24 atoms"<br>
<br>
I don't know how can I adjust this error.<br>
I have one more question again, this command give me a top<br>
file, if<br>
I want gro file of this pdb (drug that has removed from<br>
drug-enzyme<br>
complex) how can I do that?<br>
<br>
you zou wrote:<br>
> Dear Users,<br>
> > I have one question about Drug-Enzyme Complex,Similar<br>
to tutorial If I<br>
<br>
><br>
want to use GROMOS96 43a1, I can use "Prodrg Beta version"<br>
for drug > but If I want to use OPLS-AA/L all-atom force<br>
field I can use "Prodrg > Beta version" server too, or not?<br>
<br>
No. You can't use two different force fields in one<br>
simulation system.<br>
<br>
<br>
<br>
> If I can't use this server, how can I make .gro file and<br>
.itp file for > drug that remove from initial .pdb file?<br>
><br>
There are several programs in the User Contributions from the<br>
website, x2top<br>
<br>
(which is distributed with Gromacs), or you can build the<br>
topology by hand. No matter what you choose, you need a<br>
thorough understanding of the mechanics of your chosen force<br>
field, methods of validation, and of course Chapter 5 in the<br>
<br>
Gromacs manual.<br>
<br>
<br>
Thanks<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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