Re: RetinalTop

From: Ale Gomez (agomez.fisica_at_epn.edu.ec)
Date: Tue Aug 03 2010 - 11:22:19 CDT

Thanks everyone of you.... I really appreciate your help!.
Until now, everything looks fine thanks for your suggestions but It is
running the first "step" when just lipid tails are free. But I have
another inquiry, in namd membrane tutorial they always use this parameters:
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
how much is reasonable to increase these parameters?? I already know what
each parameter means, but I am not completely sure how much could be
increase it to get good results?.
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 3 August 2010 03:23, <tillmann.utesch_at_mail.tu-berlin.de> wrote:

> Hi,
>
> I think you have an atom named CR* in your parameter file, where '*' is
> treated as wildcat. So CR* equals CR14, CR15 and so on. Maybe you have to
> change the entries in your parameter file.
>
>
> Quoting Ale Gomez <agomez.fisica_at_epn.edu.ec>:
>
> 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/<
>>> http://www.ciencias.epn.edu.ec/%7Ebiomod/>
>>>
>>>
>>>
>>> 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/<
>>>> http://www.ciencias.epn.edu.ec/%7Ebiomod/>
>>>>
>>>>
>>>>
>>>> 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
>>>>>
>>>>
>
>
> --
> Tillmann Utesch
> Institut für Chemie, Max-Volmer-Laboratorium
> TU Berlin, PC 14
> Straße des 17. Juni 135
> D-10623 Berlin
> Tel. +49-(0)30-314-26389
>
>

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