[gmx-users] pdb2gmx -water-> grompp

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 19 00:19:19 CEST 2009

Paymon Pirzadeh wrote:
> Well,
> 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

The only time that [defaults] should appear is in the force field that you are 
calling (i.e., ffoplsaa.itp):



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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list