[gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system

[Justin A. Lemkul]

On 6/6/12 3:09 AM, Sangita Kachhap wrote:
>
> Hello all
> I have to do MD simulation of membrane protein having docked ligand in POPC
> lipid bilayer.
> I am geeting error during solvation of system:
> Resname of 1POPC in system_shrink1.gro converted into 1LIG
>
>
> I have done following:
>
> GROMACS COMMAND
>
> 1) Generate topol.top using GROMOS96 53A6 parameter set
> pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc
>
>
> at prompt select 14
>
> 2) Download:
>      * popc128.pdb - the structure of a 128-lipid POPC bilayer
>      * popc.itp - the moleculetype definition for POPC
>      * lipid.itp - Berger lipid parameters
>
> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>
> 3) Modify topol.top with:
> #include "gromos53a6.ff/forcefield.itp"
>
> to:
>
> #include "gromos53a6_lipid.ff/forcefield.itp"
>
>
>                  &
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> ; Include ligand topology
> #include "ligand-full.itp"
>
> ; Include POPC chain topology
> #include "popc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
> and at the end add LIG  1 in [molecules]
>
> 4) cp files
> aminoacids.rtp
> aminoacids.hdb
> aminoacids.c.tdb
> aminoacids.n.tdb
> aminoacids.r2b
> aminoacids.vsd
> ff_dum.itp
> ffnonbonded.itp
> ffbonded.itp
> forcefield.itp
> ions.itp
> spc.itp
> watermodels.dat
>
> from gromacs top to directory named gromos53a6_lipid.ff in working directory.
> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from
> lipid.itp to ffnonbonded.itp&  ffbonded.itp and create a forcefield.doc file
> that contains a description of the force field parameters contain "GROMOS96 53A6
> force field, extended to include Berger lipid parameters".
> Delete line ";; parameters for lipid-GROMOS interactions." and its subsequent
> line, change HW as H of [ nonbond_params ]
>
>
> 5) Generate .tpr for POPC
> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1
> (change OW1, HW2, HW3 to OW, HW and HW2 respectively)
>
>
> 6) Remove periodicity
> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact
> (at command prompt select 0)
>
>
> 7) Oriant the protein within the same coordinate as written in end of
> popc128a_whole.gro
> editconf -f 3gd8-mod-processed.gro -o 3gd8-mod-processe_newbox.gro -c -box
> 6.23910 6.17970 6.91950
>
>
> 8) Pack lipid around protein
> cat 3gd8-mod-processe_newbox.gro popc128a_whole.gro>  system.gro
>
> Remove unnecessary lines (the box vectors from the KALP structure, the header
> information from the DPPC structure and update the second line of the
> coordinate file (total number of atoms) accordingly.
>
> 9) Modify topol.top to add positional restrain on protein
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> ; Include DPPC chain topology
> #include "dppc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
>               &
> Genrate new positional restraint
> genrestr -f 3gd8-mod-processe_newbox.gro -o strong_posre.itp -fc 100000 100000
> 100000
> for system (protein + ligand)
> Add a line "define = -DSTRONG_POSRES" to .mdp file
>
>
> 10) addion POPC 128 to topol.top
>
>
> 11) Scale down lipid
> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat
>
>
>
> 12) Solvate with water
>
> Copy vdwradii.dat from Gromacs top to working directory and change the value of
> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)
>
> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p
> topol.top
>
>
> Upto 11th step .gro file is OK conatin protein resid 32-254, ligand 1LIG, POPC
> resid 1-128 and solvent
>
> After 12th step in gro file protein is there 32-254, Ligand 1LIG but POPC resid
> 2-128 because resid 1 of POPC is converted to 1LIG though all cordinate and atom
> name are same of 1POPC in 1LIG.
>
>
>
> Anybody please suggest me why this change in rename is occuring.
>

Based on the description, you say in step (3) that you add "LIG 1" to the end of 
[molecules], but then in (12) you give the order as protein, ligand, then POPC. 
  The order of the coordinate file and [molecules] must match, otherwise funny 
things happen.  If you have protein, ligand, and POPC, you must list the 
moleculetype names in that order in [molecules].

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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