[gmx-users] topolbuild error (marzieh dehghan)

[Justin Lemkul]

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On 5/5/14, 3:20 AM, marzieh dehghan wrote:
>   Dear Justin Lemkul
>
> Hi
>
>   thank you for your kind answer
>
> according to your advice, we changed #include "fftest.itp" to "#include
> "oplsaa.ff/fftest.itp" in the test.top.
>
> fftest.itp contains the following cases:
>
> ; topolbuild version 1.3
> ; Command line:
> ;     /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
> /home/Hossein/Desktop/topolbuild1_3/dat/gromacs -ff oplsaa
> ;
> #define _FF_OPLS
> #define _FF_OPLSAA
> #define _FF_USER
>
> [ defaults ]
> ;nbfunc     comb-rule      gen-pairs     fudgeLJ      fudgeQQ
>    1               3               yes             0.5     0.5
>
> #include "ffoplsaanb.itp"
>
>
>   test.top contains the following cases:
>
> ;
> ; Topology from .mol2 file
> ; topolbuild version 1.3
> ; Command line:
> ;     /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
> /home/Hossein/Desktop/topolbuild1_3/dat/gromacs -ff oplsaa
> ;
> ; The force field files to be included
> #include "oplsaa.ff/fftest.itp"
>
>   [ moleculetype ]
> ; name  nrexcl
> insulin2.pdb   3
>
> unfortunately after writing "grompp -f ions.mdp -c test.gro -p test.top -o
> ions.tpr
>
> I confronted the new error "topology include file "oplsaa.ff/fftest.itp"
> not found
>
>
>
>
>
> I am looking forward to getting your guidance.
>

OK, so let's back up.  You've got a modified force field that tries to use 
parameters from OPLS-AA.  So of course fftest.itp is not going to exist in the 
stock oplsaa.ff directory unless you moved it there.  The important point is 
that ffoplsaanb.itp does not exist and has not been named that for several 
years.  If your fftest.itp needs those parameters, then the #include statement 
in fftest.itp needs to be changed to #include "oplsaa.ff/ffnonbonded.itp"

-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

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