[gmx-users] Problem in setup energy minimization step(grompp)

[X Rules]

> Date: Mon, 26 Jul 2010 07:26:04 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem in  setup energy minimization step(grompp)
> 
> 
> 
> X Rules wrote:
> > Precisely,
> > 
> > open your xyz.top file and search for #include "spc.itp" and replace 
> > this line with #include "tip4p.itp"
> > 
> > and you will be done with.
> > 
> 
> Not if the coordinates present are for a three-point water model, in which case 
> the same error is occurring.  If you're switching models like this, you have to 
> re-build the system.

agreed, but I build my system entirely for tip4p, i.e adding tip4p using genbox and still my top file contains spc.itp instead of tip4p.itp (possible bug?? in 4.0.5 alteast). 

> 
> -Justin
> 
> > 
> > 
> >  > Date: Mon, 26 Jul 2010 07:00:57 -0400
> >  > From: jalemkul at vt.edu
> >  > To: gmx-users at gromacs.org
> >  > Subject: Re: [gmx-users] Problem in setup energy minimization 
> > step(grompp)
> >  >
> >  >
> >  >
> >  > bipin.singh at research.iiit.ac.in wrote:
> >  > >
> >  > > Hi all,
> >  > > I am facing a problem when i tried the TIP4P water model
> >  > > for the set up of energy minimization using grompp.
> >  > > This error did'nt occur while using the spce model.
> >  > >
> >  > > Fatal error:
> >  > > number of coordinates in coordinate file (1.pdb, 31975)
> >  > > does not match topology (1.top, 24795)
> >  > > Please help me to rectify this problem.
> >  > >
> >  >
> >  > So all you did was change the water model? That would certainly 
> > explain it,
> >  > since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise:
> >  >
> >  > 
> > http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
> >  >
> >  > -Justin
> >  >
> >  > > Thanks
> >  > > Bipin
> >  >
> >  > --
> >  > ========================================
> >  >
> >  > Justin A. Lemkul
> >  > Ph.D. Candidate
> >  > ICTAS Doctoral Scholar
> >  > MILES-IGERT Trainee
> >  > Department of Biochemistry
> >  > Virginia Tech
> >  > Blacksburg, VA
> >  > jalemkul[at]vt.edu | (540) 231-9080
> >  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >  >
> >  > ========================================
> >  > --
> >  > gmx-users mailing list gmx-users at gromacs.org
> >  > http://lists.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
> > 
> > ------------------------------------------------------------------------
> > Hotmail is redefining busy with tools for the New Busy. Get more from 
> > your inbox. See how. 
> > <http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2>
> > 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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
 		 	   		  
_________________________________________________________________
Hotmail is redefining busy with tools for the New Busy. Get more from your inbox.
http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100726/e52ba8ed/attachment.html>