[gmx-users] grompp error
Mark.Abraham at anu.edu.au
Tue Feb 10 06:15:08 CET 2009
Q. Y. HUAN wrote:
> Dear Justion,
> I pack the molecules of A, B, .......H together using Packmol (named as md.pdb)
> then i proceed to pdb2gmx (opls-aa) and editconf.
> in genbox, I planned to insert another 92 molecules ( T80 ) into the system by edit the .top file.
> You can notice that i added "" #include "T80.itp" in the top file.
> and I ran genbox by this command
> genbox -cp md.gro -cs -ci T80.pdb -nmol 92 -o md.gro -p md.top
> the T80 and water were successfully added but the error appeared in the grompp step.
> So, what is the problem of the system?
> Justin, thanks for your suggestions
> here is the .top file:
> Include forcefield parameters
> #include "ffoplsaa.itp"
> ; Include chain topologies
> #include "md_A.itp"
> #include "md_B.itp"
> #include "md_C.itp"
> #include "md_D.itp"
> #include "md_E.itp"
> #include "md_F.itp"
> #include "md_G.itp"
> #include "md_H.itp"
> ; Include water topology
> #include "spc.itp"
> #include "T80.itp"
The position restraints section below "belongs" to the waters, and needs
to be part of the same [ molecule ] section. Each of the above .itp
files defines a different [ molecule ] section, which doesn't get
terminated by the end of the file. So swapping the two lines above will
fix this problem. This is not the issue you are having, however.
As Justin suggested in his 3rd guess about your problem, at least one of
the above .itp files (probably T80) is using a CH3 atom type. This is
not defined in OPLS-AA. Mixing force fields is a bad idea - see
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> ; Include generic topology for ions
> #include "ions.itp"
> [ system ]
> ; Name
> Built with Packmol
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> Protein_B 1
> Protein_C 1
> Protein_D 1
> Protein_E 1
> Protein_F 1
> Protein_G 1
> Protein_H 1
> T80 92
> QIU YI HUAN
> A beginner of Gromacs user.
> --- On Tue, 2/10/09, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> From: Justin A. Lemkul <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] grompp error
>> To: scottiehuan at yahoo.com, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Date: Tuesday, February 10, 2009, 11:19 AM
>> Q. Y. HUAN wrote:
>>> Dear all.
>>> I wanted to run grompp in order to perform Em, but it
>> showed me this fatal errer::
>>> Back Off! I just backed up mdout.mdp to
>>> checking input for internal consistency...
>>> calling /usr/bin/cpp...
>>> processing topology...
>>> Generated 332520 of the 332520 non-bonded parameter
>>> Generating 1-4 interactions: fudge = 0.5
>>> Generated 332520 of the 332520 1-4 parameter
>>> Cleaning up temporary file grompptz9Dth
>>> Program grompp_d, VERSION 3.3.3
>>> Source code file: toputil.c, line: 61
>>> Fatal error:
>>> Atomtype 'CH3' not found!
>>> what is the error and where the source code file
>> There are several possibilities for this error:
>> 1. You haven't included the proper force field file
>> (ff*.itp) in your topology.
>> 2. You have otherwise mangled the format such that grompp
>> simply cannot find the parameters it is looking for.
>> 3. You are using atom types that do not exist within the
>> force field you wish to use.
>> Without more information about your system, we can only
>>> QIU YI HUAN
>>> A beginner of Gromacs user.
>>> gmx-users mailing list gmx-users at gromacs.org
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>> -- ========================================
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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