From: tillmann.utesch_at_mail.tu-berlin.de
Date: Tue Aug 03 2010 - 03:23:22 CDT
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/
>>
>>
>> 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
-- 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:00 CST