The force fields have to be compatible but this way works fine.<br><br><div class="gmail_quote">On 19 May 2010 12:50, 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;">
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! :)<br>
</blockquote>
<br></div>
Combining different force fields into a single system completely invalidates it, so yes, I'd say you're doing something wrong :)<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;">
<br>
;<br>
; This is your topology file<div><div></div><div class="h5"><br>
; "What If None Of Your Dreams Come True ?" (E. Costello)<br>
;<br>
; Include forcefield parameters<br>
#include "ffamber99sb.itp"<br>
<br>
[ atomtypes ] ------------------------------------------------------------------------------------from 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 "protein.itp"------------------------------------------------------------------------------------from the top file of the amber force field, contains everything 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 "trisacc.itp"------------------------------------------------------------------------------------from 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></div></div>
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>>><div class="im"><br>
<br>
Hi Justin,<br>
<br>
Thank you for your help, But when I run x2top command there 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 file, if<br>
I want gro file of this pdb (drug that has removed from 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 to tutorial If I <br>
<br>
><br>
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?<br>
<br>
No. You can't use two different force fields in one simulation system.<br>
<br>
<br>
<br>
> If I can't use this server, how can I make .gro file and .itp file for > drug that remove from initial .pdb file?<br>
> <br>
There are several programs in the User Contributions from the website, x2top <br>
<br>
(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 <br>
<br>
Gromacs manual.<br>
<br>
<br>
Thanks<br>
<br>
<br>
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<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>
<br>
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