Re: RetinalTop

From: Ale Gomez (agomez.fisica_at_epn.edu.ec)
Date: Mon Aug 02 2010 - 20:00:49 CDT

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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