From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Thu Mar 05 2009 - 17:05:51 CST
Brittany,
Can you verfiy that in the topology and parameters of top_all27_p_n_new.inp
(or possibly the psf; but if they're in the topology definition they should
be in the psf) some angle definitions and vdW parameters are not missing
that "hold" the hydrogen in place WRT the amine nitrogen and prevent the
hydrogen's "vdW" bulk from "overlapping" the neighboring carbon atom?
C.
--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078
On Thu, Mar 5, 2009 at 7:56 AM, Brittany Morgan <brmorgan_at_clarku.edu> wrote:
> Hi Chris,
>
>
>
> Here is the psfgen input script:
>
>
>
> topology /home/brittanym/topparnew/top_all27_p_n_new.inp
>
>
>
> pdbalias residue HIS HSD
>
>
>
> pdbalias atom MET H HN
>
> pdbalias atom MET HB2 HB1
>
> pdbalias atom MET HB3 HB2
>
> pdbalias atom MET HG2 HG1
>
> pdbalias atom MET HG3 HG2
>
>
>
> pdbalias atom GLN H HN
>
> pdbalias atom GLN HB2 HB1
>
> pdbalias atom GLN HB3 HB2
>
> pdbalias atom GLN HG2 HG1
>
> pdbalias atom GLN HG3 HG2
>
>
>
> pdbalias atom LYS H HN
>
> pdbalias atom LYS HB2 HB1
>
> pdbalias atom LYS HB3 HB2
>
> pdbalias atom LYS HD2 HD1
>
> pdbalias atom LYS HD3 HD2
>
> pdbalias atom LYS HE2 HE1
>
> pdbalias atom LYS HE3 HE2
>
> pdbalias atom LYS HG2 HG1
>
> pdbalias atom LYS HG3 HG2
>
>
>
> pdbalias atom GLY H HN
>
> pdbalias atom GLY HA2 HA1
>
> pdbalias atom GLY HA3 HA2
>
>
>
> pdbalias atom ASN H HN
>
> pdbalias atom ASN HB2 HB1
>
> pdbalias atom ASN HB3 HB2
>
>
>
> pdbalias atom PHE H HN
>
> pdbalias atom PHE HB2 HB1
>
> pdbalias atom PHE HB3 HB2
>
>
>
> pdbalias atom ARG H HN
>
> pdbalias atom ARG HB2 HB1
>
> pdbalias atom ARG HB3 HB2
>
> pdbalias atom ARG HD2 HD1
>
> pdbalias atom ARG HD3 HD2
>
> pdbalias atom ARG HG2 HG1
>
> pdbalias atom ARG HG3 HG2
>
>
>
> pdbalias atom THR H HN
>
> pdbalias atom ALA H HN
>
> pdbalias atom VAL H HN
>
>
>
> pdbalias atom CYS H HN
>
> pdbalias atom CYS HB2 HB1
>
> pdbalias atom CYS HB3 HB2
>
>
>
> pdbalias atom GLU H HN
>
> pdbalias atom GLU HB2 HB1
>
> pdbalias atom GLU HB3 HB2
>
> pdbalias atom GLU HG2 HG1
>
> pdbalias atom GLU HG3 HG2
>
>
>
> pdbalias atom HIS H HN
>
> pdbalias atom HIS HB2 HB1
>
> pdbalias atom HIS HB3 HB2
>
>
>
> pdbalias atom ILE H HN
>
> pdbalias atom ILE CD1 CD
>
> pdbalias atom ILE HG12 HG11
>
> pdbalias atom ILE HG13 HG12
>
> pdbalias atom ILE HD11 HD1
>
> pdbalias atom ILE HD12 HD2
>
> pdbalias atom ILE HD13 HD3
>
>
>
> pdbalias atom PRO HB2 HB1
>
> pdbalias atom PRO HB3 HB2
>
> pdbalias atom PRO HD2 HD1
>
> pdbalias atom PRO HD3 HD2
>
> pdbalias atom PRO HG2 HG1
>
> pdbalias atom PRO HG3 HG2
>
>
>
> pdbalias atom TRP H HN
>
> pdbalias atom TRP HB2 HB1
>
> pdbalias atom TRP HB3 HB2
>
>
>
> pdbalias atom ASP H HN
>
> pdbalias atom ASP HB2 HB1
>
> pdbalias atom ASP HB3 HB2
>
>
>
> pdbalias atom SER H HN
>
> pdbalias atom SER HB2 HB1
>
> pdbalias atom SER HB3 HB2
>
> pdbalias atom SER HG HG1
>
>
>
> pdbalias atom LEU H HN
>
> pdbalias atom LEU HB2 HB1
>
> pdbalias atom LEU HB3 HB2
>
>
>
> pdbalias atom TYR H HN
>
> pdbalias atom TYR HB2 HB1
>
> pdbalias atom TYR HB3 HB2
>
>
>
> segment VTS {pdb VTS_U.pdb; first NONE; last CTER; auto none}
>
> coordpdb VTS_U.pdb VTS
>
>
>
> writepsf VTSU.psf
>
> writepdb VTSU.pdb
>
>
>
>
>
>
>
>
>
>
>
>
>
> The NAMD configuration file:
>
>
>
>
>
> structure /home/morganb/vtsu/vtsu.solv.psf
>
> coordinates /home/morganb/vtsu/vtsu.solv.pdb
>
> outputName ./min/vts.output
>
>
>
> set temperature 298
>
>
>
> firsttimestep 0
>
>
>
>
>
> #############################################################
>
> ## SIMULATION PARAMETERS ##
>
> #############################################################
>
>
>
> # Input
>
> paraTypeCharmm on
>
> parameters /home/morganb/par_all27_p_n_new.inp
>
>
>
> # 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 {1} {
>
> cellBasisVector1 54. 0. 0.
>
> cellBasisVector2 0. 54. 0.
>
> cellBasisVector3 0. 0. 54.
>
> cellOrigin 0.35 -0.93 1.59
>
> }
>
> wrapWater on
>
> wrapAll on
>
> zeroMomentum no ; #can use for NVE
>
>
>
>
>
> # Force-Field Parameters
>
> exclude scaled1-4
>
> 1-4scaling 1.0
>
> cutoff 12.
>
> switching on
>
> switchdist 10.
>
> pairlistdist 13.5
>
>
>
>
>
> # Integrator Parameters
>
> timestep 0.5 ;# 2fs/step
>
> #rigidBonds all ;# needed for 2fs steps
>
> nonbondedFreq 1
>
> fullElectFrequency 1
>
> stepspercycle 10
>
>
>
>
>
> #PME (for full-system periodic electrostatics)
>
> if {1} { # For speed, grid sizes should only have factors of 2, 3 and 5
>
> PME yes
>
> PMEGridSizeX 54
>
> PMEGridSizeY 54
>
> PMEGridSizeZ 54
>
> PMEGridSpacing 1.0
>
> }
>
>
>
>
>
> # Constant Temperature Control
>
> langevin on ;# do langevin dynamics
>
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
>
> langevinTemp $temperature
>
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
>
>
>
>
> # Constant Pressure Control (variable volume)
>
> if {1} {
>
> useGroupPressure yes ;# needed for 2fs steps
>
> useFlexibleCell no ;# 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 100.
>
> langevinPistonDecay 50.
>
> langevinPistonTemp $temperature
>
> }
>
>
>
>
>
> restartfreq 2000 ;# 500steps = every 1ps
>
> dcdfreq 100
>
> xstFreq 2000
>
> outputEnergies 100
>
> outputPressure 100
>
> #velDCDfreq 100
>
>
>
>
>
>
>
> #############################################################
>
> ## EXECUTION SCRIPT ##
>
> #############################################################
>
>
>
> # Minimization
>
> if {1} {
>
> minimize 5000; # Number of force evaluations
>
> reinitvels $temperature
>
> }
>
>
>
> run 0;
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> *From:* charris5_at_gmail.com [mailto:charris5_at_gmail.com] *On Behalf Of *Chris
> Harrison
> *Sent:* Wednesday, March 04, 2009 8:41 PM
> *To:* Brittany Morgan
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: Minimization convergence issue
>
>
>
> If you are using a script as input to psfgen, can you paste the script in a
> reply email? Can you also paste the namd configuration file. Sounds like
> something could be wrong with angle, vdW, etc definitions in the psf or
> parameters read-in during NAMD's startup.
>
>
> C.
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
>
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