Dear gromacs users, <br>
Well I looked at my created topology file and it was like this:<br>
<br>
<br>
;<br>
; File 'minimized_2water.top' was generated<br>
; By user: simulant (1000)<br>
; On host: lvt-uni-e09-3<br>
; At date: Fri Oct 7 13:47:39 2005<br>
;<br>
; This is your topology file<br>
; LYSOZYME<br>
;<br>
; Include forcefield parameters<br>
#include "ffG43a1.itp"<br>
<br>
; Include chain topologies<br>
#include "minimized_2water_A.itp"<br>
#include "minimized_2water_B.itp"<br>
<br>
; Include water topology<br>
#include "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 generic topology for ions<br>
#include "ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
LYSOZYME<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
Protein_B 1<br>
SOL 10017<br>
SOL 10017<br>
<br>
<br>
A topology file should be a lot bigger, at least it was what I
realized looking to the topology of my protein(aki.top). So
shouldn´t be there also the informations about my protein?? I
mean, what do I have to do with this "part" of topology created, should
I include this to my other topology file (aki.top)? Any help would be
greateful, as I wrote before I am a new user, it´s the first time that
I try to do this, I mean, to update a topology file.<br>
Thank you very much in advance!<br>
Fernando Mattio<br><br><div><span class="gmail_quote">2005/10/7, Fernando Mattio <<a href="mailto:mattiofer@gmail.com">mattiofer@gmail.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<span class="q"> Thank you Elena,<br>
I think the topology was updated, but I had problems
related to "Memory access error" when i used the mdrun to perform the
simulation... So I was wondering if it is not enough memory of my
computer or if I should have somehow updated also the parameter file...
Please gromacs users any information about would be great,<br>
Thanks in advance,<br>
Fernando Mattio.<br><br></span><div><span class="q"><span class="gmail_quote">2005/10/7, elena.papaleo <<a href="mailto:elena.papaleo@unimib.it" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
elena.papaleo@unimib.it</a>>:</span></span><div><span class="e" id="q_106cb1ed53eaa154_3"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Fernando,<br>I think you can use the command pdb2gmx -f<br>minimized_2water.gro -p minimized_2water.top<br>to update your topology file...<br>best regard<br>Elena Papaleo<br><br><br>Elena Papaleo, PhD Student<br>Department of Biotechnology and Biosciences
<br>University of Milano-Bicocca<br>P.zza della Scienza 2, 20126 Milano (Italy)<br><br>email: <a href="mailto:elena.papaleo@unimib.it" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">elena.papaleo@unimib.it
</a><br>phone: +39 0264483475<br></blockquote></span></div></div><br>
</blockquote></div><br>