[gmx-users] Problem in Molecular dynamics of ligand protein complex in POPC lipid

[Justin Lemkul]

On 7/22/14, 2:13 AM, neha bharti wrote:
> Hello All
>
> I an trying molecular dynamics simulation of ligand protein complex in popc
> lipid with charmm36 force field and also follow Justin tutorial. But in
> that tutorial its only for protein not for ligand protein complex. I also
> took help of Justin protein-ligand complex tutorial. But while performing
> energy minimization step in  "Pack the lipids around the protein " its
> giving following error:
>
> Fatal error:
> Syntax error - File cyc.itp, line 7
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
>
>
> my topology file is :
>
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
>
> ; Include ligand topology
> #include "cyc.itp"
>
> ; Ligand position restraints
> #ifdef POSRES
> #include "posre_cyc.itp"
> #endif
>
>
> ; Include POPC chain topology
> #include "popc.itp"
>
> ; Include water topology
> #include "charmm36.ff_lipid/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_lipid/ions.itp"
>
> [ system ]
> ; Name
> Protein in Lipid
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> LIG            1
> POPC                128
>
>
>
> I also check my changing the position of LIG and POPC like
>
> POPC    128
> LIG     1
>
> But it still giving the same error..
>
> Can any one please help me out for this..
>

The ligand introduces new atom types; the topology format requires that all atom 
types be declared before any [moleculetype] is invoked, so that all of the 
nonbonded and bonded parameters are known before any molecules are constructed 
using those parameters.  Move your #include statement for the ligand right after 
the #include statement for the force field, before the protein [moleculetype] 
and this should fix it.

>
> Is there any tutorial for ligand protein complex in lipid???
>

There isn't anything particularly special here; it's just a minor variation on a 
theme and all the same principles apply.

-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

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