[gmx-users] Unable to neutralize my system

[Berk Hess]

Hi,

Just a sideremark, but are you sure you want to solvate your ~6000 atom
protein in a box with nearly 3 million water molecules?

Berk.



> Date: Thu, 8 May 2008 16:04:20 +0530
> From: namita at ncbs.res.in
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Unable to neutralize my system
> 
> Dear All
> 
> When I run the command "genion" specifying the number n type of chrges to
> be added, it works fine. I also have made changes in my topology file. But
> somwhow when I run the "grompp" after that it gives me the following
> error...
> 
> processing topology...
> Generated 380 of the 1326 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 2818600
> Excluding 1 bonded neighbours for Na+ 2
> NOTE:
>   System has non-zero total charge: -2.399999e+01
> 
> processing coordinates...
> -------------------------------------------------------
> Program grompp_mpi, VERSION 3.3.1
> Source code file: grompp.c, line: 448
> 
> Fatal error:
> number of coordinates in coordinate file (ce_myoII_frag0_neu.gro, 8461523)
>              does not match topology (ce_myoII_frag0.top, 8461535)
> -------------------------------------------------------
> 
> I tried adding 2 and 3 ions to the system. But it seems to give the same
> error. Could someone help?
> 
> Thanks
> Namitha Mohandas
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080508/6f933ec6/attachment.html>