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Dear Sir,<br>
Thank you for your kind reply. I have one polymer with sidegroup
which contains OH group. Is there any provision in Gromacs where I can
remove the bond between O and H, and add Na+ ion at the H's position,
so that it will be O- and Na+. If I can do this please tell me
how I can? Thanking you in advance.<br>
<br>
Rahul Karyapa<br>
NCL, India<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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