<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Just a sideremark, but are you sure you want to solvate your ~6000 atom<br>protein in a box with nearly 3 million water molecules?<br><br>Berk.<br><br></div><br><br><hr id="stopSpelling">> Date: Thu, 8 May 2008 16:04:20 +0530<br>> From: namita@ncbs.res.in<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Unable to neutralize my system<br>> <br>> Dear All<br>> <br>> When I run the command "genion" specifying the number n type of chrges to<br>> be added, it works fine. I also have made changes in my topology file. But<br>> somwhow when I run the "grompp" after that it gives me the following<br>> error...<br>> <br>> processing topology...<br>> Generated 380 of the 1326 non-bonded parameter combinations<br>> Excluding 3 bonded neighbours for Protein 1<br>> Excluding 2 bonded neighbours for SOL 2818600<br>> Excluding 1 bonded neighbours for Na+ 2<br>> NOTE:<br>> System has non-zero total charge: -2.399999e+01<br>> <br>> processing coordinates...<br>> -------------------------------------------------------<br>> Program grompp_mpi, VERSION 3.3.1<br>> Source code file: grompp.c, line: 448<br>> <br>> Fatal error:<br>> number of coordinates in coordinate file (ce_myoII_frag0_neu.gro, 8461523)<br>> does not match topology (ce_myoII_frag0.top, 8461535)<br>> -------------------------------------------------------<br>> <br>> I tried adding 2 and 3 ions to the system. But it seems to give the same<br>> error. Could someone help?<br>> <br>> Thanks<br>> Namitha Mohandas<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>