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

[Justin A. Lemkul]

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.

-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

========================================