[gmx-users] Atomtype OW_tip4p not found

[Justin A. Lemkul]

On 6/6/12 7:36 AM, Amir Abbasi wrote:
>
>
> --------------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Amir Abbasi <amir.abbasi69 at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> *Sent:* Wednesday, June 6, 2012 3:58 PM
> *Subject:* Re: [gmx-users] Atomtype OW_tip4p not found
>
>
>
> On 6/6/12 7:19 AM, Amir Abbasi wrote:
>  > Hi!
>  > I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then I
>  > generate .gro and .top files of that with amb2gmx.pl <http://amb2gmx.pl>.
>  > I'm manually add this lines to .top file
>  > ; Include water topology
>  > #include "amber99sb.ff/tip4p.itp"
>  >
>  > ; Include topology for ions
>  > #include "amber99sb.ff/ions.itp"
>  > but after running this code:
>  >
>  > grompp -f ions.mdp -c ribozyme_solv.gro -p ribozyme.top -o ions.tpr
>  > I've got this error message:
>  >
>  > Program grompp, VERSION 4.5.5
>  > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1166
>  >
>  > Fatal error:
>  > Atomtype OW_tip4p not found
>  >
>  > what should I do?
>  >
>
> If I recall my Amber evolution correctly, parmbsc0 and Amber99SB are different
> entities, so you may have some inconsistencies in your force field calls. Which
> of the Amber force fields in Gromacs have you called (earlier in the topology)?
> The OW_tip4p atom type exists in Amber99SB, so I don't know the origin of the
> error.
>
> -Justin
>
> I've Removed these lines from .top file
>
> ; Include water topology
> #include "amber99sb.ff/tip4p.itp"
>
> ; Include topology for ions
> #include "amber99sb.ff/ions.itp"
> But this error occured:
>
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987
>
> Fatal error:
> No such moleculetype SOL
>
> what's the true way to add solvent molecules to my system?
> I want to use parmbsc0 ff that's not included in gromacs and I use it with amb2gmx
>

Please answer the question posted above by posting a relevant topology snippet. 
  It's hard (impossible) to help you while working in the dark.  Presumably you 
have some force field you are calling - what is it?

Removal of these lines will not solve the problem, as you can see.  You need to 
#include a water model of some sort to define what parameters water will have, 
but it needs to be consistent with whatever force field you are using or have 
otherwise constructed.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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