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Respected Sir,<br>
I am generating my structure (.pdb) using Cerius2
software. There I am putting my model in the box and performing energy
minimization. As you told I first removed Na+ ions from the .pdb
file. Then I generated .gro and .top files using PRODRG website. Then I
added Na+ ions again in the .gro file. But my question is where to add
Na+ ions in the .top file? In the beginning of the file I added
#include "ions.itp" and in the last like this:<br>
[ system ]<br>
; Name<br>
Protein<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein 1<br>
SOL 182 <br>
Na 10 <br>
But after this when I ran grompp it gave me following errors:<br>
<font size="2">processing coordinates...<br>
Warning: atom names in topol.top and out1.gro don't match (OW - NAA)<br>
Warning: atom names in topol.top and out1.gro don't match (HW1 - NAB)<br>
Warning: atom names in topol.top and out1.gro don't match (HW2 - NAC)<br>
Warning: atom names in topol.top and out1.gro don't match (OW - NAD)<br>
......<br>
<br>
<font size="3">And when I ran mdrun it gave me following errors:<br>
<br>
</font>Back Off! I just backed up step5.pdb to ./#step5.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
Warning: 1-4 interaction between 15 and 20 at distance larger than 1 nm<br>
These are ignored for the rest of the simulation<br>
turn on -debug for more information<br>
<br>
Back Off! I just backed up step6.pdb to ./#step6.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
<br>
Back Off! I just backed up step7.pdb to ./#step7.pdb.1#<br>
Wrote pdb files with previous and current coordinates<br>
<br>
</font>Where am I going wrong? Is it correct? Or I need to add them where we specify other atoms in the .top file.<br>
waiting for your kind reply.<br>
Rahul Karyappa<br>
NCL, Pune<br>
<br><font face="Arial" size="2"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><b><i>-- Original Message --</i></b><br>From: David van der Spoel <spoel@xray.bmc.uu.se><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Date: Mon, 05 Sep 2005 09:06:03 +0200<br>Subject: Re: [gmx-users] problem with Na+ ions....<br><br><br>On Mon, 2005-09-05 at 11:41 +0530, Rahul Karyappa wrote:<br>> Dear all,<br>> I have structure with defined Na ions in it. I have a .pdb file of<br>> that structure and I want to convert it to .gro and .top files. When I<br>> tried it on PRODRG website it gave me error that Na+ is not supported.<br>> Then I defined all the atoms in .rtp file also Na. But it's not<br>> working. What can I do for this? I have included "ions.itp" file in<br>> the .top file. Do I need to delete the Na+ entry in the .top file. I<br>> can't delete them from .gro file because their coordinates are<br>> specified. What Should I do?<br>take out Na from your pdb file, make the topology and add the Na back in<br>manually. check chap. 5 in the manual.<br>> Thanking you in advance.<br>> <br>> Rahul Karyappa<br>> NCL, India<br>> *****************************************************************<br>> This email is virus free by TrendMicro Inter Scan Security Suite.<br>> *****************************************************************<br>> <br>> _______________________________________________<br>> gmx-users mailing list<br>> gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>-- <br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br>spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br><br>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br><br>*****************************************************************<br>This email is virus free by TrendMicro Inter Scan Security Suite.<br>*****************************************************************<br></TD></TR></tbody></TABLE></font></BODY></HTML>
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