Re: RetinalTop

From: Ale Gomez (agomez.fisica_at_epn.edu.ec)
Date: Mon Aug 02 2010 - 22:53:13 CDT

I really appreciate your help Basak!
I started all over again including your suggestions and untill now looks
fine. I am only concern about one warming in log file during the first
"step", when only lipid tails are free to move. I get this message:

Warning: VDW TYPE NAME CR15 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR14 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR13 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR12 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR11 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR10 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR9 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR8 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR7 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR6 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR5 MATCHES PARAMETER TYPE NAME CR*
Warning: Ignored 444 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.

Any suggestion??.
Kind Regards

-------------------------------------------------------------------
Ale Gómez
Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/

On 2 August 2010 21:52, Basak Isin <isinbasak_at_yahoo.com> wrote:

> Hi Ale,
> Do you keep getting the unstable atoms from the same area of the system?
> Did you check if they are overlapping with some other atoms in the system?
> There may be some steric clashes that can not be fixed by minimization and
> equilibration. If lipids or water molecules are too close to the protein
> atoms, it would be better to remove them rather than trying to stabilize
> them by minimization or equilibration.
> I would also be good to use 1 fs timestep for preparation steps of the
> system. 2fs timestep can then be used for the production runs.
> That is all I can think of. But I still don't consider myself as an expert
> in MD simulations. :o)
> Good luck,
> Basak
>
>
> ------------------------------
> *From:* Ale Gomez <agomez.fisica_at_epn.edu.ec>
> *To:* Basak Isin <isinbasak_at_yahoo.com>; namd-l <namd-l_at_ks.uiuc.edu>
> *Sent:* Mon, August 2, 2010 9:00:49 PM
>
> *Subject:* Re: namd-l: RetinalTop
>
> Hi Basak and thanks for your help. I assume that you had worked with
> rhodopsin systems and probably you could help me a little. I tried to
> simulate a system with bacteriorhodopsin in a lipid membrane. I read the
> Membrane Protein Tutorial from the NAMD webpage but I can't get over the
> second step in simulation, i.e. when I fixed just the protein and some water
> molecules. When I ran it, I always had one atom unstable. That is why I
> started all over again, trying to fix any warming message.
> But still I can not made it. After 1000 minimization steps I, I had again
> an unstable atom. Could be the tcl forces script, keep_water_out.tcl????.
> Thanks in advance for your help.
> My configuration file is:
>
> #############################################################
> ## JOB DESCRIPTION ##
> ############################################################
> # Min. and Eq. of bR
> # embedded in POPC membrane, ions and water.
> # Protein constrained. PME, Constant Pressure.
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ../Preparacion/bRET_popcwi.psf
> coordinates ../Preparacion/bRET_popcwi.pdb
> outputName bRET_popcwimineq-02
>
> set temperature 300
>
> # Continuing a job from the restart files
> if {1} {
> set inputname bRET_popcwimineq-01
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> extendedSystem $inputname.restart.xsc
> }
>
> firsttimestep 251000
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../par_all27_prot_lipidNBFIX.prm
>
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> #temperature $temperature
>
>
> # Periodic Boundary Conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> #if {0} {
> #cellBasisVector1 77. 0. 0.
> #cellBasisVector2 0. 77. 0.
> #cellBasisVector3 0. 0. 90.
> #cellOrigin 0.285711854696 0.299352765083 6.22171497345
> #}
> wrapWater on
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSizeX 80
> PMEGridSizeY 80
> PMEGridSizeZ 90
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell yes ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
>
> restartfreq 1000 ;# 1000steps = every 2ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 50
> outputPressure 50
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> #if {0} {
> #fixedAtoms on
> #fixedAtomsFile nottails.fix.pdb
> #fixedAtomsCol B
> #fixedAtomsForces on
> #}
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
>
> constraints on
> consexp 2
> consref ../Preparacion/bRET_popcwi.pdb
> conskfile bRET_popcwi.cnst
> conskcol B
> margin 3
>
> tclforces on
> set waterCheckFreq 100
> set lipidCheckFreq 100
> set allatompdb ../Preparacion/bRET_popcwi.pdb
> tclForcesScript keep_water_out.tcl
>
> #eFieldOn yes
> #eField 0 0 -0.155
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {1} {
> minimize 1000
> reinitvels $temperature
> }
>
> run 250000 ;# 0.5 ns
> -------------------------------------------------------------------
> Ale Gómez
> Biophysics and Molecular Modeling Group
> Physics Department
> Escuela Politécnica Nacional, Quito - Ecuador
> Ladrón de Guevara E11-253.
> Casilla 17-01-1253
> http://www.ciencias.epn.edu.ec/~biomod/>
>
>
> On 2 August 2010 15:55, Basak Isin <
isinbasak_at_yahoo.com> wrote:
>
>> Hi Ale,
>> I don't know how it is in bacteriarhodopsin but in rhodopsin retinal is
>> covalently bound to Lys 296. Lyr in the topology and parameter files should
>> contain a lysine crosslinked retinal. If this crosslink exists in
>> bacteriorhodopsin, you should rename both Lys and retinal as LYR. You should
>> also make sure that you have all of the atoms necessary for this link and
>> remove any extra atoms.
>> good luck,
>> Basak
>>
>> ------------------------------
>> *From:* Ale Gomez <agomez.fisica_at_epn.edu.ec>
>> *To:* namdlist_at_gmail.com
>> *Cc:* namd-l <namd-l_at_ks.uiuc.edu>
>> *Sent:* Mon, August 2, 2010 12:07:52 PM
>> *Subject:* Re: namd-l: RetinalTop
>>
>> Hi Bjoern and thanks for your help.
>> In my pdb file (1C3W), retinal's resname is RET and in the repository file
>> is a resname LYR. I know that retinal is linked with LYS 216 and I do not
>> sure If I should change it in my pdb file. Should I change just the RET
>> resname or LYS 216 too?.
>> I tried change both to LYR and running vmd, and I think works fine. But
>> when I tried to minimize my system with NAMD I found this messages:
>> Warning: VDW TYPE NAME CR15 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR14 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR13 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR12 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR11 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR10 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR9 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR8 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR7 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR6 MATCHES PARAMETER TYPE NAME CR*
>> Warning: VDW TYPE NAME CR5 MATCHES PARAMETER TYPE NAME CR*
>>
>> It could be a reason that my system became unstable???.
>> Thanks for your help and sorry about the cross post.
>>
>> -------------------------------------------------------------------
>> Ale Gómez
>> Biophysics and Molecular Modeling Group
>> Physics Department
>> Escuela Politécnica Nacional, Quito - Ecuador
>> Ladrón de Guevara E11-253.
>> Casilla 17-01-1253
>> http://www.ciencias.epn.edu.ec/~biomod/>
>>
>>
>> On 2 August 2010 09:49, Bjoern Olausson <
namdlist_at_googlemail.com> wrote:
>>
>>> On Monday 02 August 2010 15:52:10 Ale Gomez wrote:
>>> > Hi everyone.
>>> > I am trying to simulate bacteriorhodopsin in a lipid membrane but in
>>> charmm
>>> > topology there is not topology for retinal. I found this
>>> >
>>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?ParameterTopologyReposi
>>> > tory but
>>> > I am not sure how should I use it. I have to just add it into the
>>> topology
>>> > file I am using??. Same situation for parameter file.
>>> > Thanks in Advance
>>> > Kind Regards
>>> >
>>>
>>> Don't cross post to VMD.
>>>
>>> In NAMD you can load the Retinal parameter file additional to your
>>> current
>>> parameter file file.
>>>
>>> #######################
>>> paraTypeCharmm on
>>> parameters ../par_all27_prot_lipid.prm
>>> parameters ../retinal.prm
>>> #######################
>>>
>>>
>>> In CHARMM you have to load both par/top file. When loading the Retinal
>>> topology file, take care that the Retianl topology file does not contain
>>> any
>>> overlapping MASS values. If it happens to have overlapping MASS entries,
>>> change them but then you have to regenerate your PSF to reflects the
>>> changed
>>> MASS entries. So merge the retinal top/par files with your current
>>> top/par
>>> files and change the MASS entries for Retinal not to contain duplicates.
>>>
>>> Read more in the CHARMM-Forum about this topic:
>>>
>>> http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24193#Post24193
>>>
>>> Cheers
>>> Bjoern
>>>
>>> --
>>> Bjoern Olausson
>>> Martin-Luther-Universität Halle-Wittenberg
>>> Fachbereich Biochemie/Biotechnologie
>>> Kurt-Mothes-Str. 3
>>> 06120 Halle/Saale
>>>
>>> Phone: +49-345-55-24942
>>>
>>
>>
>>
>
>

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