Dear Justin, <br><br>Thank you. Problem is solved. I forgot remove ions from SOL numbers.<br>By the way, I used the genion command as "genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log" but it correctly worked.<br>
<br>Thanks<br><br><br><br><div class="gmail_quote">16 Nisan 2011 21:37 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear users,<br>
<br>
I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then I started to simulation .I met such a problem ( last error) after I added ions. What could be the problem?<br>
pdb2gmx -f withoutligand_xxx.pdb<br>
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro<br>
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro<br>
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr<br>
<br>
*Fatal Error:*<br>
System has non-zero total charge: -1.500000e+01<br>
<br>
genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log<br>
</blockquote>
<br></div>
Unless you updated your topology manually after running this command, you haven't accounted for the fact that 15 water molecules are going to be removed. Use the -p flag to have genion make the changes for you. Note that "NA+" is incorrect for version 4.5.3 - ion [moleculetype] names have changed since version 4.0.7.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
select: Group 13 (SOL)<br>
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr<br>
*Fatal error:*<br>
number of coordinates in coordinate file (solvated.gro, 106473)<br>
does not match topology (topol.top, 106518)<br>
<br>
</blockquote>
<br></div>
The answer to this error is _always_ the same - you haven't accounted properly for some change in the system that has been made to the coordinate file but not the topology.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology" target="_blank">http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology</a><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
_*topol.top:*_<div class="im"><br>
..<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
Protein_chain_B 1<br>
SOL 185<br>
SOL 143<br>
SOL 33723<br>
NA 15<br>
<br>
</div></blockquote>
<br>
Something isn't matching up here. Either your genion command that you showed above is wrong, or this topology snippet has been modified from what genion would produce. Please always copy and paste commands, topology snippets, etc so that we have self-consistent information to help you.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
-- <br>
Ahmet YILDIRIM<br>
<br>
</blockquote>
<br>
-- <br>
========================================<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.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>