<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>
Dear Sir,<br>
Thank you for your kind reply. I removed Na ions from the .rtp entry. When I ran pdb2gmx it gave me following error:<br><font face="Arial" size="2"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><font size="2"><i>Fatal error: Atom NA10 in residue PAA 2 not found in rtp entry with 10 atoms<br>
while sorting atoms<br>
<br>
What shouls I do now? Thanking you once again.<br>
<br>
Rahul Karyappa<br>
NCL, India<br>
</i></font><b><i><br>
ORIGINAL Message--<br>
<br>
</i></b><br>From: David <spoel@xray.bmc.uu.se><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Date: Sat, 03 Sep 2005 13:45:47 +0200<br>Subject: Re: [gmx-users] chargegroups????????<br><br>On Sat, 2005-09-03 at 16:57 +0530, Rahul Karyappa wrote:<br>> Dear all,<br>> I am new to Gromacs. Since one nomth I am trying to run my<br>> models on Gromacs. But I am not 100% successeful. Using PRODRG website<br>> I am able to crate .gro and .top files and also I am able to run MD<br>> run on them. But when create them using gromacs commands I am still<br>> not successful. I think I am making mistakes while defining the .rtp<br>> parameters. My partial .pdb file looks like this:<br>> <br>> REMARK 4 Poly COMPLIES WITH FORMAT V. 2.0 <br>> HETATM 1 HT PAA 1 -0.423 6.910 -1.504 1.00 0.00<br>> H <br>> HETATM 2 C1 PAA 1 0.155 6.563 -2.363 1.00 0.00<br>> C <br>> HETATM 3 C2* PAA 1 1.609 6.203 -1.930 1.00 0.00<br>> C <br>> HETATM 4 C3 PAA 1 1.609 5.131 -0.899 1.00 0.00<br>> C <br>> HETATM 5 O1 PAA 1 1.237 3.954 -1.147 1.00 0.00<br>> O1-<br>> HETATM 6 2HC PAA 1 2.037 7.095 -1.462 1.00 0.00<br>> H <br>> HETATM 7 1H1C PAA 1 -0.339 5.686 -2.789 1.00 0.00<br>> H <br>> HETATM 8 1H2C PAA 1 0.157 7.352 -3.119 1.00 0.00<br>> H <br>> HETATM 9 O2 PAA 1 2.122 5.306 0.227 1.00 0.00<br>> O <br>> HETATM 10 NA10 PAA 2 3.217 2.864 -0.095 1.00 0.00<br>> NA1+<br>> This in one repeat unit of the polymer surrounded by sodium ions.<br>> While including the atoms in the .rtp file I am including them for one<br>> repeat unit. But when I run pdb2gmx it says there are missing atoms. I<br>> think while mentioning the charge group I am making mistake. I have<br>> given 1 as a charge group for the atoms and 2 for sodium ion. But<br>> chargegroup are different for remaining repeat units. Is this the<br>> problem or anything else is there? Do I need to specify atosm for all<br>> the repeat units?<br><br>Don't put the Na+ in the rtp since it is not covalently bound. pdb2gmx<br>probably complanis about the termini: run with flag -ter and select None<br>for N- and C-terminus.<br><br><br>> please help me out?<br>> Thanking you in advance. please answer this question. It's very<br>> important for me.<br>> <br>> Rahul Karyappa<br>> NCL, India<br>> <br>> <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>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></TD></TR></tbody></TABLE></font></BODY></HTML>
<table><tr><td bgcolor=#ffffff><font color=#000000>*****************************************************************<br>
This email is virus free by TrendMicro Inter Scan Security Suite.<br>
*****************************************************************<br>
</font></td></tr></table>