Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
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"
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
Message-ID:<4fcf5364@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 10
10
10
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
[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > >1. Re: Re: change in rename of 1POPC to 1LIG thoughcoordinate > 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 pressurecoupling > (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" > 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 > Message-ID: <4fcf5364@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
Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
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 10 10 10 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 "LIG1" 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 -- Justin A. Lemkul, Ph.D. Research Scien
[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
> gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: Question regarding genion (Justin A. Lemkul)
>2. Re: change in rename of 1POPC to 1LIG though coordinate and
> atom same in 1LIG of 1POPC, during solvation of system
> (Justin A. Lemkul)
>3. Re: Scaling/performance on Gromacs 4 (Manu Vajpai)
>4. Atomtype OW_tip4p not found (Amir Abbasi)
>
>
> --
>
> Message: 1
> Date: Wed, 06 Jun 2012 06:04:43 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Question regarding genion
> To: Discussion list for GROMACS users
> Message-ID: <4fcf2b3b.30...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
>
>
> On 6/6/12 5:38 AM, Matthias Ernst wrote:
>> Hi,
>>
>> I have to questions regarding genion.
>>
>> 1) Is there a possibility to tell genion in advance which group of molecules
>> to
>> replace by ions (for me, solvent is always the choice so I want to skript it
>> but
>> I did not find any parameters for this)?
>>
>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
>> 2) I want to neutralize a charged system. Therefore, as I found out, I can
>> use
>> the -neutral option. But it seems to me that this option does not work if I
>> do
>> not specify a concentration (system has a charge of -52):
>> genion -s system_in_solvent.tpr -o solventions.gro -p topol_water.top
>> -neutral
>> [snap]
>> Reading file system_in_solvent.tpr, VERSION 4.5.4 (single precision)
>> Using a coulomb cut-off of 1 nm
>> No ions to add and no potential to calculate.
>>
>> If I use genion {parameters as above} -conc 0.0 it also won't add ions but if
>> I
>> try e.g. genion {parameters as above} -c 0.0001, it will add 52 NA and 0 CL
>> ions
>> which corresponds to a neutral system (with -c 0.001, it will add 53 NA and 1
>> CL
>> ions, meaning resulting salt concentration is > 0). I use the amber99sb
>> forcefield.
>> Is this behaviour desired and do I miss the point of the -neutral option not
>> working without specifying a concentration?
>>
>
> I have also found that -neutral must always be used in conjunction with -conc.
> It would be nice if this were not the case.
>
> -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
>
>
>
>
> --
>
> Message: 2
> Date: Wed, 06 Jun 2012 06:08:55 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] 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
> Message-ID: <4fcf2c37.4040...@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> 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.
