[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
Sangita Kachhap
sangita at imtech.res.in
Wed Jun 6 19:12:29 CEST 2012
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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.
>
> -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, 6 Jun 2012 14:06:27 +0100
> From: Steven Neumann <s.neumann08 at gmail.com>
> Subject: [gmx-users] Segmentation fault - pdb2gmx specbond.dat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAKZJqQGScStS2BPZtLKBjREmOiWvk_JtCa3f_JWrE_AT6RZePw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gmx Users,
>
> I created a plane surface made of 4 different atoms (400 atoms togehter).
> Each atom correspond to different residue - I added them to the
> aminoacids.rtp file. They are placed in different positions with LJ radius
> of 1.7A and they their center is 3.6 A away from each other (0.2A between
> atom LJsurfaces). I want to create bonds between all of them so I added
> specbonds.dat to my working directory:
>
> 10
> POS SOD 4 POS SOD 4 0.36 POS POS
> POS SOD 4 NEG CLA 4 0.36 POS NEG
> POS SOD 4 POL N 4 0.36 POS POL
> POS SOD 4 NON C 4 0.36 POS NON
> NEG CLA 4 NEG CLA 4 0.36 NEG NEG
> NEG CLA 4 POL N 4 0.36 NEG POL
> NEG CLA 4 NON C 4 0.36 NEG NON
> POL N 4 POL N 4 0.36 POL POL
> POL N 4 NON C 4 0.36 POL NON
> NON C 4 NON C 4 0.36 NON NON
>
> So that all of them can create bonds with each of them being within the
> distance of 3.6A. When I process to pdb2gmx where the matrix is created and
> bonds are being linked when the last residues are linked:
>
> .....
> Linking POL-397 N-397 and NEG-398 CLA-398...
> Linking NEG-398 CLA-398 and NON-399 C-399...
> Linking NON-399 C-399 and POL-400 N-400...
> Segmentation fault (core dumped)
>
> The Gromacs is installed on the cluster - version 4.5.5. I tried also on
> 4.5.4. and the same happens.
>
> Could you please advise?
>
> Steven
> -------------- next part --------------
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> ------------------------------
>
> Message: 3
> Date: Wed, 06 Jun 2012 15:07:40 +0200
> From: Anja Kuhnhold <anja.kuhnhold at physik.uni-halle.de>
> Subject: [gmx-users] energy conservation: shift vs shifted user
> potential
> To: gmx-users at gromacs.org
> Message-ID: <fab69db81004c.4fcf723c at uni-halle.de>
> Content-Type: text/plain; charset=us-ascii
>
> Dear gmx-users,
>
> I have a problem concerning energy conservation when using user potentials
> (tables).
> I'm using gromacs 4.5.4
> I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 chains a 10
> beads in a 26x26x26 periodic box).
>
> I tried different vdwtypes (cutoff always 3.24):
> The cut-off version does not conserve energy -- okay.
> The shift and switch versions conserve energy -- fine.
>
> Now I wanted to do the same with user tables:
> Simple Lennard-Jones table gives really the same results as the cut-off version
> -- good.
>
> But if I use a table with shifted Lennard-Jones potential it is not comparable
> to the shift version
> and the energy is not conserved -- ?
>
> I use a shift function as written in the manual (chapter 4.1.5) -- there must be
> a factor alpha added in the constants A and B --
> (r1=0).
>
> The parameters are the same for shift version and shifted user version.
>
> Has someone an idea why the shifted user potential doesn't work in this way?
>
> Here is the mdp:
>
>
> integrator = md-vv
> dt = 0.0035
> nsteps = 1000
> nstxout = 1
> nstvout = 1
> nstfout = 1
> nstlog = 1
> ns_type = grid
> pbc = xyz
> rvdw = 3.24
> rlist = 3.6
> tcoupl = no
> tc-grps = System
> tau_t = 2.0
> ref_t = 127.2717
> vdwtype = user;Shift
> rcoulomb = 3.6;2.24;1.12
> coulombtype = Cut-off
> rvdw-switch = 0.0
>
> energygrps = bead
> energygrp_table = bead bead
>
>
> Thanks in advance
> Anja
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 6 Jun 2012 18:07:45 +0300
> From: Bao Kai <paeanball at gmail.com>
> Subject: [gmx-users] Cannot get correct pressure value with MTTK
> pressure coupling
> To: gmx-users at gromacs.org
> Message-ID:
> <CAGCCrwGCuJEwZt=m5fjqvemuSda08+kxvukrionScruoOUjJuQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> HI, all,
>
> I want to use MTTK for the pressure coupling for NPT simulation, while
> I can not get the correct pressure value.
>
> The following result is a simulation with 1000 SPC-E water molecules
> with temperature 303.15K and pressure 1 bar.
>
> Statistics over 1000001 steps [ 0.0000 through 1000.0000 ps ], 3 data sets
> All statistics are over 200001 points
>
> Energy Average Err.Est. RMSD Tot-Drift
> -------------------------------------------------------------------------------
> Temperature 303.155 0.016 5.54033 0.0532334 (K)
> Pressure 138.295 1.3 429.699 -5.68756 (bar)
> Density 1002.82 0.24 8.04912 0.668867 (kg/m^3)
> .
>
> The following is the mdp file
>
> title = fizzy water
> ; Run parameters
> integrator = md-vv ; velocity-verlet integrator
> nsteps = 1000000; 0.001 * 1000000 = 1000 ps, 1 ns
> dt = 0.001 ; 2 fs
>
> ; Output control
> nstxout = 1000 ; save coordinates every 2 ps. Incr by *10
> nstvout = 1000 ; save velocities every 2 ps. Incr by *10
> nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps. Incr by *10
> nstenergy = 1000 ; save energies every 2 ps. Incr by *10
> nstlog = 1000 ; update log file every 2 ps. Incr by *10
>
> ; Bond parameters
> continuation = yes ; <-- Restarting after NPT
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
>
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 0.9 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
> rvdw = 0.9 ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
>
> ; Temperature coupling is on
> tcoupl = nose-hoover ; modified Berendsen thermostat
> tc-grps = System ; two coupling groups - more accurate
> tau_t = 0.1 ; time constant, in ps
> ref_t = 303.15 ; reference temperature, one for each group, in K
>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; turning on pressure coupling
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; <-- Pressure coupling is on
> pcoupl = mttk; Pressure coupling on in NPT
> nstpcouple = 1;
> pcoupltype = isotropic ; uniform scaling of box vectors
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
>
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> ; Velocity generation
> gen_vel = no ; <-- Velocity generation is off
> ;
>
> Could anybody tell me anything wrong with my configuration?
>
> Thank you very much.
>
> Best Regards,
> Kai
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 06 Jun 2012 11:13:25 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Cannot get correct pressure value with MTTK
> pressure coupling
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FCF7395.6090209 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 6/6/12 11:07 AM, Bao Kai wrote:
>> HI, all,
>>
>> I want to use MTTK for the pressure coupling for NPT simulation, while
>> I can not get the correct pressure value.
>>
>> The following result is a simulation with 1000 SPC-E water molecules
>> with temperature 303.15K and pressure 1 bar.
>>
>> Statistics over 1000001 steps [ 0.0000 through 1000.0000 ps ], 3 data sets
>> All statistics are over 200001 points
>>
>> Energy Average Err.Est. RMSD Tot-Drift
>> -------------------------------------------------------------------------------
>> Temperature 303.155 0.016 5.54033 0.0532334 (K)
>> Pressure 138.295 1.3 429.699 -5.68756 (bar)
>> Density 1002.82 0.24 8.04912 0.668867 (kg/m^3)
>> .
>>
>> The following is the mdp file
>>
>> title = fizzy water
>> ; Run parameters
>> integrator = md-vv ; velocity-verlet integrator
>> nsteps = 1000000; 0.001 * 1000000 = 1000 ps, 1 ns
>> dt = 0.001 ; 2 fs
>>
>> ; Output control
>> nstxout = 1000 ; save coordinates every 2 ps. Incr by *10
>> nstvout = 1000 ; save velocities every 2 ps. Incr by *10
>> nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps. Incr by *10
>> nstenergy = 1000 ; save energies every 2 ps. Incr by *10
>> nstlog = 1000 ; update log file every 2 ps. Incr by *10
>>
>> ; Bond parameters
>> continuation = yes ;<-- Restarting after NPT
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
>> lincs_iter = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>>
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> rlist = 0.9 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
>> rvdw = 0.9 ; short-range van der Waals cutoff (in nm)
>>
>> ; Electrostatics
>> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>> pme_order = 4 ; cubic interpolation
>> fourierspacing = 0.16 ; grid spacing for FFT
>>
>> ; Temperature coupling is on
>> tcoupl = nose-hoover ; modified Berendsen thermostat
>> tc-grps = System ; two coupling groups - more accurate
>> tau_t = 0.1 ; time constant, in ps
>> ref_t = 303.15 ; reference temperature, one for each group, in K
>>
>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>> ; turning on pressure coupling
>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>> ;<-- Pressure coupling is on
>> pcoupl = mttk; Pressure coupling on in NPT
>> nstpcouple = 1;
>> pcoupltype = isotropic ; uniform scaling of box vectors
>> tau_p = 2.0 ; time constant, in ps
>> ref_p = 1.0 ; reference pressure, in bar
>> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
>>
>> ; Periodic boundary conditions
>> pbc = xyz ; 3-D PBC
>>
>> ; Dispersion correction
>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>
>> ; Velocity generation
>> gen_vel = no ;<-- Velocity generation is off
>> ;
>>
>> Could anybody tell me anything wrong with my configuration?
>>
>
> Probably nothing. Pressure is a very hard term to converge, as noted here:
>
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> Note that the manual warns that you will get very large oscillations in the
> pressure value if you don't start from a reasonable (i.e., previously
> equilibrated) value. Using Berendsen for initial NPT equilibration is more
> common and more stable.
>
> Your simulations are also very short. Pressure (and other terms) may require
> more than just 1 ns to converge, but you should also bear in mind that the value
> you obtained is 138.295 ? 429.699. Is that significantly different from the
> target value? Given the magnitude of the standard deviation, I would say no.
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
>
> End of gmx-users Digest, Vol 98, Issue 37
> *****************************************
>
With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
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