<br><br><div class="gmail_quote">On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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>
On 5/29/12 6:52 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Ok. My topology:<br>
<br>
; Include forcefield parameters<br>
#include "./charmm27.ff/forcefield.itp"<br>
<br>
; Include ligand topology<br>
#include "ligand1.itp"<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_1<br>
#include "posre_ligand1.itp"<br>
#endif<br>
<br>
; Include ligand topology<br>
#include "ligand2.itp"<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_2<br>
#include "posre_ligand2.itp"<br>
#endif<br>
<br>
; Include ligand topology<br>
#include "ligand3.itp"<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_3<br>
#include "posre_ligand3.itp"<br>
#endif<br>
<br>
; Include ligand topology<br>
#include "ligand4.itp"<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_4<br>
#include "posre_ligand4.itp"<br>
#endif<br>
<br>
<br>
; Include ligand topology<br>
#include "ligand5.itp"<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_5<br>
#include "posre_ligand5.itp"<br>
#endif<br>
<br>
; Include ligand topology<br>
#include "ligand6.itp"<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES_6<br>
#include "posre_ligand6.itp"<br>
#endif<br>
<br>
; Include water topology<br>
#include "./charmm27mod.ff/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 topology for ions<br>
#include "./charmm27.ff/ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
Protein in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
ligand1 1<br>
ligand2 1<br>
ligand3 1<br>
ligand4 1<br>
ligand5 1<br>
ligand6 1<br>
SOL 4617<br>
<br>
<br>
Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information<br>
is the same<br>
<br>
posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.<br>
<br>
Then when I grompp:<br>
<br>
Syntax error - File ligand2.itp, line 7<br>
Last line read:<br>
'[ atomtypes ] '<br>
Invalid order for directive atomtypes<br>
<br>
Any suggestions appreciated,<br>
<br>
</blockquote>
<br></div></div>
Once you declare a [moleculetype], the other force field-level directives cannot be called. If all the ligand topologies are the same, remove [atomtypes] from all but the first.<div class="HOEnZb"><div class="h5"><br>
<br>
-Justin<br></div></div></blockquote><div><br>Thanks Justin. Removing [pairtypes] and [atomtypes] from all but not the first helped.<br><br>Steven<br><br><br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="HOEnZb"><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><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>==========<br>
-- <br>
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