[gmx-users] Atomtype OW_tip4p not found

[Justin A. Lemkul]

On 6/7/12 6:18 PM, Amir Abbasi wrote:
>
>
> --------------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wednesday, June 6, 2012 4:08 PM
> *Subject:* Re: [gmx-users] Atomtype OW_tip4p not found
>
>
>
> On 6/6/12 7:36 AM, Amir Abbasi wrote:
>  >
>  >
>  > --------------------------------------------------------------------------------
>  > *From:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *To:* Amir Abbasi <amir.abbasi69 at yahoo.com <mailto:amir.abbasi69 at yahoo.com>>;
> Discussion list for GROMACS users
>  > <gmx-users at gromacs.org <mailto: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>
> <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
> this is my topology file (generated by amb2gmx_dihed_old.pl):
>
> ; rna.top created by rdparm2gmx.pl Thu May 24 19:07:56 IRDT 2012
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5 0.8333
>
> [ atomtypes ]
> ;name bond_type mass charge ptype sigma epsilon
> HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00
> NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01
> H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02
> N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01
> CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01
> OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01
> CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01
> C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01
> CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01
> NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01
> O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01
> CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01
> H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02
> O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01
> P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01
> H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02
> HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02
> H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02
> H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02
>
> [ moleculetype ]
> ; Name nrexcl
> solute 3
> there is not any force field included. I want to use parmbsc0 ff thats not
> included in gromacs. I build topology file in tleap (part of ambertools) then
> convert it to gromacs topology file.
>
>

Then you need to add all appropriate parameters for the missing atom types.  As 
you can see from the [atomtypes] directive above, you have not declared 
OW_tip4p.  Anything that you need to use later on must be declared at the 
beginning of the topology.  See Chapter 5 of the manual for the required format 
and sequence of directives.

-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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