[gmx-users] Error in free energy calculation

[Justin Lemkul]

On 3/16/17 5:49 AM, Tasneem Kausar wrote:
> Dear All
>
> I am trying to perform free energy calculations of a protein drug system.
> I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug
> molecule is defined in separate drug.itp file. From the discussions of
> mailing list I have found that this is not a problem. To obtain the
> equilibrium values for protein-ligand restraint 15 ns simulation was
> performed. Here is the last section of topology file.
>  ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> #include "drug.itp"
> [ intermolecular_interactions ]
> [ bonds ]
> ;    i     j  type     r0A     r1A     r2A    fcA    r0B     r1B     r2B
> fcB
>   1444  3118    10     0.591   0.591   10.0   0.0    0.591   0.591   10.0
> 4184.000
>
> [ angle_restraints ]
> ;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB
> multB
>   1431  1444  3118  1444     1    52.35    0.0    1    52.35    41.840    1
>   1444  3118  3120  3118     1   118.14    0.0    1   118.14    41.840    1
>
> [ dihedral_restraints ]
> ;   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB
> fcB
>   1444  1431  1444  3118     1    -99.41   0.0    0.0    -99.41    0.0
> 41.840
>   1431  1444  3118  3120     1     17.49    0.0    0.0    17.49    0.0
> 41.840
>   1444  3118  3120  3119     1     -6.49   0.0    0.0     -6.49    0.0
> 41.840
> ; Include water topology
> #include "gromos54a7.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 topology for ions
> #include "gromos54a7.ff/ions.itp"
>
> [ system ]
> ; Name
> DUMM in water t= 10000.00000
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DRG                 1
> SOL             17685
>
> Is there any default position for [ intermolecular_interaction ] in
> topology file.

The [intermolecular_interactions] directive uses global atom numbering, and as 
such it must follow [system] so that this numbering can be established.

> Since I am using a drug.itp file for drug molecule. Numbering in itp file
> starts from 1. Is atom number in itp file needed to be modified?
>
>
> grompp gives many warning  and 1 error
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
>
> WARNING 1 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_geometry' in parameter file
>

Here, you're using outdated syntax.  See the manual for proper keywords.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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