Hi Brian,
This is the sequence of commands I used in tleap:
source leaprc.ff99SBildn
loadAmberParams frcmod.ff99SBnmr
WAT = T4E
set WAT.1 name "T4E"
loadAmberParams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew
loadoff tip4pewbox.off
set default FlexibleWater on
mol = loadpdb protein.pqr
addIons2 mol Na+ 90 Cl- 101
solvateOct mol TIP4PEWBOX 15.1
setBox mol vdw
savePDB mol protein.amber.pdb
saveAmberParm mol protein.prmtop protein.inpcrd
quit
This is the POINTERS section of my prmtop:
%FLAG
POINTERS
%FORMAT(10I8)
129517 19 96235 33109 35154 2084 6961 5382
0 0
238260 31925 33109 2084 5382 50 100 70
35 1
0 0 0 0 0 0 0 1
24 0
31551
%FLAG
SOLVENT_POINTERS
%FORMAT(3I8)
374 31745 195
How can the prmtop be wrong if I AMBER starts from a truncated octahedron
box?
thanks,
Thomas
On 31 January 2013 22:58, Brian Radak <radak004.umn.edu> wrote:
> Hi Thomas,
>
> The lattice vectors you provide are for an orthorhombic box, not a
> truncated octahedron. Was your prmtop generated by leap using solvateOct?
> What is the value of IFBOX in the prmtop (it should be 2 or 3)? This is in
> the POINTERS section, the 3rd last value on line 3 I believe.
>
> Regards,
> Brian
>
> On Thu, Jan 31, 2013 at 3:21 PM, Thomas Evangelidis <tevang3.gmail.com
> >wrote:
>
> > I guess this is what you mean:
> >
> > trajin cMDrun1.prod_TIP4PEw.nc
> > center :1-162 mass origin
> > image origin center familiar
> > trajout cMDrun1.prod_TIP4PEw.wrapped.nc netcdf
> > go
> >
> > The protein residues are numbered 1-162. The trajectory doesn't change,
> it
> > seems that the barostast applies pressure over the 6 planes of a cube(?)
> > instead on the 12 planes of a truncated octahedron (?). There must be
> > something wrong with the parameters I am using because the .prmtop and
> .rst
> > files look normal to me. Below is the last line of my restart (.rst) file
> > from which I resumed the simulation. It was an NVT equilibration without
> > restraints.
> >
> > 115.6172820 135.3319607 138.3907610 90.0000000 90.0000000 90.0000000
> >
> > I am also quoting again the relevant configuration parameters:
> >
> >
> > ntxo=2, ! write binary NetCDF restart files
> > ioutfm=1, ! use binary NetCDF format for the coordinate and velocity
> > trajectory files (mdcrd, mdvel and inptraj).
> > iwrap=1, ! wrap coordinates into primary box
> >
> > ! TEMPERATURE CONTROL
> > tempi =100.0, ! initial temperature
> > temp0=300.0, ! reference temperature at which the system is to be
> > kept, if ntt > 0
> > ntt=3, ! Use Langevin thermostat.
> > gamma_ln=5, ! Damping coefficient for Langevin dynamics in ps - 1.
> > tautp=2.0, ! Time constant, in ps, for heat bath coupling for the
> > system, if ntt = 1
> > ig=209858, ! The seed for the pseudo-random number generator
> >
> > ! PRESSURE CONTROL
> > ntb=2, ! use constant pressure
> > ntp=1, ! use pressure coupling
> >
> >
> > Any idea what's wrong?
> >
> >
> > Thomas
> >
> >
> >
> > On 31 January 2013 14:54, David A Case <case.biomaps.rutgers.edu> wrote:
> >
> > > On Thu, Jan 31, 2013, Thomas Evangelidis wrote:
> > > >
> > > > I ran a short simulation with pmemd.cuda using the following
> parameters
> > > but
> > > > the truncated octahedron was gradually reshaped to a parallelepiped
> > box.
> > > Am
> > > > I doing something wrong?
> > >
> > > Doens't sound like it. There are various ways to represent a truncated
> > > octahedron. If you want to view the results as an ocatahedron, use the
> > > "familiar" keyword in the image command in ptraj or cpptraj.
> > >
> > > ...dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> >
> > ======================================================================
> >
> > Thomas Evangelidis
> >
> > PhD student
> > University of Athens
> > Faculty of Pharmacy
> > Department of Pharmaceutical Chemistry
> > Panepistimioupoli-Zografou
> > 157 71 Athens
> > GREECE
> >
> > email: tevang.pharm.uoa.gr
> >
> > tevang3.gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Jan 31 2013 - 13:30:04 PST
