[gmx-users] pdb2gmx -water-> grompp

Paymon Pirzadeh ppirzade at ucalgary.ca
Wed Aug 19 00:17:40 CEST 2009

I changed the topology file of the system and manually typed the .itp of
my own water model. Just a reminder that I have used my own water
model's .itp file successfully in pure water systems. This .itp file
starts from [ defaults ] and contains all information needed. But when
it comes to grompp, the following error appears:

Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File sixsitewater.itp, line 6
Last line read:
'[ defaults ]'
Invalid order for directive defaults

I am trying to use this water model with OPLSaa. what kind of directive
am I missing? 


On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
> Paymon Pirzadeh wrote:
> > Hello,
> > I am trying to use a different water model for my proteins (using oplsaa
> > force field). I use the .itp file which I developed, but pdb2gmx does
> > not accept it. I am a bit confused on how I can make my water model work
> > with OPLSaa. Based on what I saw from spc.itp or other samples, do I
> > need to change the names of my particles in my water .itp file by
> > including _FF_OPLS?
> I don't know how pdb2gmx decides how to recognize water models; it may be 
> hard-coded.  In any case, your atom types have to be consistent with OPLS 
> standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file, 
> you may not need it if OPLS is the only force field with which it will be used. 
>   The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.
> -Justin
> > Regards,
> > 
> > Payman 
> > 
> > _______________________________________________
> > 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
> > 

More information about the gromacs.org_gmx-users mailing list