On 6/7/12 6:18 PM, Amir Abbasi wrote:
--------------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *To:* Amir Abbasi <amir.abbas...@yahoo.com <mailto:amir.abbas...@yahoo.com>>;
Discussion list for GROMACS users
> <gmx-users@gromacs.org <mailto:gmx-users@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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