[gmx-users] question about gromacs

[Justin Lemkul]

On 2/4/14, 8:43 AM, Andrew Bostick wrote:
> I used following line in mdp file:
>
> define      = -DPOSRES_dopc -DPOSRES_chol
>
> Is my manner true?
>

To do what?  That will trigger the #include statements in the topology, but the 
error message shown below indicates that you have not correctly created those 
.itp files.

-Justin

>
> On Tue, Feb 4, 2014 at 5:09 PM, Andrew Bostick <andrew.bostick1 at gmail.com>wrote:
>
>> Hi all
>>
>> My system contain dopc + cholesterol + water + drug molecules.
>>
>> I want to do MD simulation with position restraint on dopc and cholesterol
>> molecules.
>>
>> I used following lines to obtain posre*.itp files:
>>
>> genrestr -f npt.gro -n index.ndx -o posre_dopc.itp
>>
>> genrestr -f npt.gro -n index.ndx -o posre_chol.itp
>>
>> My topol.top file is as follows:
>>
>> ; Include forcefield parameters
>> #include "gromos-43a1-s3_lipid.ff/forcefield.itp"
>>
>> #include "cholesterol.itp"
>> #ifdef POSRES_chol
>> #include "posre_chol.itp"
>> #endif
>>
>> #include "dopc.itp"
>> #ifdef POSRES_dopc
>> #include "posre_dopc.itp"
>> #endif
>>
>> #include "gromos-43a1-s3_lipid.ff/spc.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>     1    1       1000       1000       1000
>> #endif
>>
>> #include "drug.itp"
>>
>> [ system ]
>> ; Name
>> dopc/chol/drug/sol
>>
>> [ molecules ]
>> ; Compound        #mols
>> CHOL        26
>> DOPC       102
>> drg               1
>> SOL       4677
>>
>> When I used grompp, I encountered error:
>>
>> Fatal error:
>> [ file posre_chol.itp, line 34 ]:
>> Atom index (30) in position_restraints out of bounds (1-29).
>> This probably means that you have inserted topology section
>> "position_restraints" in a part belonging to a different molecule than you
>> intended to. In that case move the "position_restraints" section to the
>> right molecule.
>>
>> I check the GROMACS website at http://www.gromacs.org/Documentation/Errors.
>> in my opinion my topol.top file is true.
>>
>> How to fix this error.
>>
>> Any help will highly appreciated.
>>
>>
>>
>>
>>

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

Justin A. Lemkul, Ph.D.
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

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