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 http://wiki.gromacs.org/index.php/Force_Fields.

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; 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 <jalem...@vt.edu> wrote:

From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] grompp error
To: scottieh...@yahoo.com, "Discussion list for GROMACS users" 
<gmx-users@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
./#mdout.mdp.1#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter
combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter
combinations
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
located?
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
guess.

-Justin
thanks


QIU YI HUAN
A beginner of Gromacs user.


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

Justin A. Lemkul
Graduate Research Assistant
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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