Re: RetinalTop

From: Ale Gomez (agomez.fisica_at_epn.edu.ec)
Date: Wed Aug 04 2010 - 11:47:09 CDT

Thank you everyone of you.
Finally, it works well without any change in cutoff parameter. I think that
I was having problems performing my system. But with your suggestions
everything seems ok.
Thanks!!!!
-------------------------------------------------------------------
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 11:22, Ale Gomez <agomez.fisica_at_epn.edu.ec> wrote:

> 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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