[gmx-users] Re: 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 8:52 AM, Sangita Kachhap wrote:

>> 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].
>>
>
>
>
>
>
> Thanks for reply
> In step 3 I added "LIG    1" to the end of [molecules] because when I used
> command "pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc" to
> generate topol.top it already contain "Protein_chain_A  1" in [molecules] so I
> added only "LIG   1"
>
>
> This is end of topol.top after solvation
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> LIG                 1
> POPC             128
> SOL              1829
>
>
>

OK, that makes sense.  Did InflateGRO remove any lipids?  If it did, that is not 
reflected correctly in the topology.

-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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