Dear Lemkul,<div><br></div><div>Thanks.</div><div><br></div><div>Can any one suggest how/where to get the correct .itp file for Guanidinium Chloride?</div><div><br></div><div>Regards</div><div>Biswajit<br><br><div class="gmail_quote">
On Tue, Mar 20, 2012 at 5:32 PM, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
Biswajit Gorai wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear GROMACS users,<br>
<br>
I am beginner to GROMACS. I want to simulate my protein in different concentrations of Guanidinium Chloride solution and collected the files (3M & 5M box and .itp file) from <a href="http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies" target="_blank">http://www.gromacs.org/<u></u>Downloads/User_contributions/<u></u>Molecule_topologies</a>. Then I build a topology file 'topol.top' (to minimize the box further) as<br>
<br>
; Include forcefield parameters<br>
#include "gromos43a1.ff/forcefield.itp"<br>
<br>
#include "gnd.itp"<br>
<br>
; Include water topology<br>
#include "gromos43a1.ff/spc.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 topology for ions<br>
#include "gromos43a1.ff/ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
Gdm 3M<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
GND 19<br>
SOL 269<br>
CL- 19<br>
<br>
Then I execute the command<br>
$ grompp -f minim.mdp -c gnd3M.gro -p topol.top -o em.tpr<br>
<br>
But I got the following error<br>
<br>
Program grompp, VERSION 4.5.5<br>
Source code file: toppush.c, line: 1631<br>
<br>
Fatal error:<br>
Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
------------------------------<u></u>-------------------------<br>
<br>
Is there something wrong with the .itp file (given) or I am doing any mistake?<br>
<br>
</blockquote>
<br></div></div>
The .itp file is wrong. With pair type 2, 5 parameters are required (FudgeQQ, qi, qj, V, and W), unlike pair type 1, which only requires 2 (V and W). See Table 5.5 in the manual for the required format.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<span class="HOEnZb"><font color="#888888"><br>
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