[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
jalemkul at vt.edu
Thu Jun 7 13:27:54 CEST 2012
On 6/6/12 1:12 PM, Sangita Kachhap wrote:
>
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>> Today's Topics:
>>
>> 1. Re: Re: change in rename of 1POPC to 1LIG though coordinate
>> and atom same in 1LIG of 1POPC, during solvation of system
>> (Justin A. Lemkul)
>> 2. Segmentation fault - pdb2gmx specbond.dat (Steven Neumann)
>> 3. energy conservation: shift vs shifted user potential
>> (Anja Kuhnhold)
>> 4. Cannot get correct pressure value with MTTK pressure coupling
>> (Bao Kai)
>> 5. Re: Cannot get correct pressure value with MTTK pressure
>> coupling (Justin A. Lemkul)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 06 Jun 2012 08:56:04 -0400
>> From: "Justin A. Lemkul"<jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though
>> coordinate and atom same in 1LIG of 1POPC, during solvation of system
>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
>> Message-ID:<4FCF5364.800 at vt.edu>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>
>>
>>
>> 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.
>
>
>
>
> No it did,nt. After using InflaterGRO it tells 64 lipid in uper leaflet and 64
> in lower leaflet so there are total 128 lipid before and after scaling down.
>
That's bizarre. Even the smallest protein should cause some lipid overlap,
unless your initial scaling factor was enormous. Also note that InflateGRO will
indeed report that there are 64 lipids per leaflet, but only later in the screen
output will it state whether or not it is removing any lipids.
The only feasible source of error I can think of is that there is a mismatch
between the coordinate and topology files, but given the information at hand I
can't see its origin. Check all your steps again carefully, verify the contents
of the coordinate file using external means (counting via grep, etc), and if all
else fails, start again, making sure of each step along the way.
-Justin
--
========================================
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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