Hi, Justin,<br>thank you for your reply.<br>I have just checked my .itp files.<br>I have 7 itp files:<br>- one is generated by doing genpr to define the restraints on the protein;<br>- six (two for each chain of my complex) are generated directly by pdb2gmx (first step of my simulation).<br>
<br>The first itp file is ok: numbers are consecutive and starting from1.<br>The other six files have not consecutive numbers (I paste here the first lines of one of these files):<br><br>[ position_restraints ]<br>; atom type fx fy fz<br>
1 1 1000 1000 1000<br> 4 1 1000 1000 1000<br> 5 1 1000 1000 1000<br> 6 1 1000 1000 1000<br> 7 1 1000 1000 1000<br><br>Since they are automatically generated by pdb2gmx, how can I fix the problem?<br>
Thank you very much.<br><br>Annalisa<br><br>
-----------------------------------------------------<br><div class="im">
Annalisa Bordogna<br>
PhD. Student<br>
DISAT - Università degli Studi di Milano Bicocca<br>
Milano - Italy<br>
-----------------------------------------------------</div><br><br><br><div class="gmail_quote">2009/4/6 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
annalisa bordogna wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi everybody,<br>
I am setting up an MD run on a peptide-protein complex with gromacs. I have defined the box and solvated the system, but now I'd like to equilibrate the solvent, so I tried with grompp, but an error occurs:<br>
<br>
Fatal error:<br>
Residue numbers in the .top are not numbered consecutively from 1<br>
<br>
I paste here my file .top:<br>
<br>
; Include forcefield parameters<br>
#include "ffG43a2.itp"<br>
<br>
; Include chain topologies<br>
#include "a.complex_A.itp"<br>
#include "a.complex_B.itp"<br>
#include "a.complex_C.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>
Protein in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
Protein_B 1<br>
Protein_C 1<br>
SOL 28799<br>
<br>
I have searched in the wiki and in the archives of the mailing list, but I have found no hints on how I could fix it.<br>
Does anybody know how can I manage to make grompp work?<br>
<br>
</blockquote>
<br></div></div>
The problem actually pertains to (at least) one of the chains you've included. Numbering is inconsistent in that file. Check the .itp files and make sure the atoms are numbered consecutively.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Thank you in advance,<br>
best regards,<br>
Annalisa<br>
<br>
-----------------------------------------------------<br>
Annalisa Bordogna<br>
PhD. Student<br>
DISAT - Università degli Studi di Milano Bicocca<br>
Milano - Italy<br>
-----------------------------------------------------<br>
<br>
<br></div>
------------------------------------------------------------------------<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<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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