[gmx-users] Atomtype OW_tip4p not found

[Amir Abbasi]

________________________________
 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>
> *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
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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120607/eb715c5a/attachment.html>