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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Have you incorrectly changed the numbers in the topology, the difference in the number is 8, so it appears your coordinate file contains 8 more atoms than the
topology. You will have to work out how that is.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Drug Discovery Biology<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Seera Suryanarayana<br>
<b>Sent:</b> Friday, 8 June 2012 3:32 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Regarding error<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear all gromacs users,<br>
<br>
While running the grompp commond after addition of counter ions i am getting the following error.<br>
<br>
Fatal error:<br>
number of coordinates in coordinate file (3ASW_ion.gro, 178301)<br>
does not match topology (3ASW.top, 178293)<br>
<br>
Here i am sending my .top file,kindly tell me how to overcome this error.<br>
<br>
<br>
<br>
<br>
<br>
;<br>
; File '3ASW.top' was generated<br>
; By user: onbekend (0)<br>
; On host: onbekend<br>
; At date: Sat Jun 9 10:36:25 2012<br>
;<br>
; This is a standalone topology file<br>
;<br>
; It was generated using program:<br>
; pdb2gmx - VERSION 4.5.5<br>
;<br>
; Command line was:<br>
; pdb2gmx -f 3ASW.pdb -o 3ASW.gro -p 3ASW.top -missing<br>
;<br>
; Force field was read from the standard Gromacs share directory.<br>
;<br>
<br>
; Include forcefield parameters<br>
#include "gromos43a1.ff/forcefield.itp"<br>
<br>
; Include chain topologies<br>
#include "3ASW_Protein_chain_A.itp"<br>
#include "3ASW_Protein_chain_B.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>
;#include "ions.itp"<br>
[ system ]<br>
; Name<br>
CLUMPING FACTOR B; TAIL REGION DERIVED PEPTIDE in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
Protein_chain_B 1<br>
SOL 129<br>
SOL 5<br>
SOL 58209<br>
NA ions 8<br>
/Add NA ions<br>
<br>
<br>
Suryanarayana Seera,<br>
JRF,<br>
India.<o:p></o:p></p>
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