[gmx-users] Unknown cmap torsion between atoms

[Justin Lemkul]

On 8/27/14, 5:20 PM, Xiang Ning wrote:
> Dear Justin,
>
> Thank you very much for your assistance. I divided the system into protein,
> lipid, water and ions, and ran pdb2gmx to obtain the top files, and converted
> the top files to itp files by deleted force filed file, [system] and [molecules]
> in the end of the top files. And then, I combine these files into one top file:
> system.top, it is like the below:
>
> ; Include forcefield parameters
> #include "./charmm36.ff/forcefield.itp"
>
> ; Include protein topology
> #include "pep.itp"
>
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include lipid topology
> #include "POP.itp"
>
> ; Include water topology
> #include "./charmm36.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy  fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "./charmm36.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> Other2              1
> SOL              1776
>
> However, there is a fatal error when I used this system.top ran "grompp -f
> minim.mdp -c system.gro -p system.top -o system.tpr":
> Syntax error - File forcefield.itp, line 9
> Last line read:
> '1      2       yes     1.0     1.0'
> Found a second defaults directive.
>
> I would like to know, how can I combine the itp files into one correct top file?
>

One or more of your .itp files has an #include "forcefield.itp" statement. 
Those need to be removed as well.  The only three differences between .itp and .top:

1. Does not #include a force field
2. Does not have [system]
3. Does not have [molecules]

An .itp is generally a standalone file for one [moleculetype], while a .top is a 
full system description, so for a proper .itp, the system-level directives must 
be omitted.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================