Re: Dihedral colvar

From: PRITI ROY (priitii.roy_at_gmail.com)
Date: Fri Sep 08 2017 - 14:33:45 CDT

Thanks for your suggestion. The NAMD error is as follows:

TCL: Suspending until startup complete.
ERROR: 'colvarsConfig' is a required configuration option
ERROR: when 'colvars' is set
ERROR: colvarsConfig defines: configuration for the collective variables
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

So if i set this option then in the the hoe to by-pass the value from NAMD
to colvar configuration file?

Best,
Priti

On Sat, Sep 9, 2017 at 12:36 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> I can see at least one mistake at the end. Your name and colvars values
> within the harmonic are flipped. Not to mention you are creating a ton of
> colvars and harmonics with the same name, and I'm pretty sure that leads to
> unintended consequences. Just an FYI, you are going to have alot more
> success if you provide the error message NAMD provides and at least try to
> parse it yourself. Saying something "is not working" creates alot of work
> for the folks who would like to help you.
> -Josh
>
> On 09/08/2017 01:01 PM, PRITI ROY wrote:
> Dear Jerome,
>
> Thank you again for giving such information. Now I have used the "tcl" in
> NAMD input file for colvar and create such type of colvar string as you
> told previously. But still this is not working. Can you please check the
> script which I copied in below where I might did some mistake.
>
> ####NAMD input file
> structure ../../c_ion.psf
> coordinates ../../c_ion.pdb
> outputname min01 #writes final .vel and .coor
>
> paraTypeCharmm on #parameter file is charmm type
> parameters /home/nsengupta/priti/restrain/par_all22_prot.prm
>
> exclude scaled1-4 #which pair is excluded from non-bonded
> inter
> 1-4scaling 1.0
> cutoff 12.5 #coulomb and vdW in Angs
> switching on #smoothing function for coulomb and vdW
> switchdist 10.5 #distance at which smooth starts (in Angs)
> pairlistdist 13.5 #goes with cutoff
>
> timestep 2.0 #timesteps are in femtoseconds
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1 #time steps between non-bonded evaluation
> restartfreq 1 #at this frequency
> dcdfile min01.dcd #writes .dcd file
> dcdfreq 500 #at this frequency
> outputEnergies 500 #writes energy at this frequency
> fullElectFrequency 2 #time steps between Coulomb evaluation
> stepspercycle 20 #atoms are reassigned every cycle
>
> PME on #use particle mesh Ewald for Coulomb
> PMEGridSpacing 1.0
>
> cellBasisVector1 118.0 0.0 0.0 #periodic boundary
> cellBasisVector2 0.0 76.0 0.0 #conditions
> cellBasisVector3 0.0 0.0 89.0
> cellOrigin 232.49 80.76 7.22
>
>
> minimization on
> numsteps 20000
>
> colvars on
>
> ###file opening containg atom index and phi/psi value
> set f1 [open "c_A.dat" r] #atom C index
> set ff1 [read $f1]
> set f2 [open "n_A.dat" r] #atom N index
> set ff2 [read $f2]
> set f3 [open "ca_A.dat" r] #atom CA index
> set ff3 [read $f3]
> set f4 [open "phi1_a.dat" r] #phi value
> set ff4 [read $f4]
>
> for {set n 0} {$n <= 54} {incr n} {
> set nxt [expr ($n + 1)]
>
> #phi
> set c1_p [lindex $ff1 $n]
> set n_p [lindex $ff2 $n]
> set ca_p [lindex $ff3 $n]
> set c2_p [lindex $ff1 $nxt]
> set p [lindex $ff4 $n]
>
> cv config "colvar {
> name phi
> dihedral {
> group1 {
> atomNumbers $c1_p
> }
> group2 {
> atomNumbers $n_p
> }
> group3 {
> atomNumbers $ca_p
> }
> group4 {
> atomNumbers $c2_p
> }
> }
> }"
>
> harmonic {
> name phi
> colvars dihedral
> centers $p
> forceConstant 5.0
> }
> }
>
>
> Best,
> Priti
>
> On Fri, Sep 8, 2017 at 7:23 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:
> jerome.henin_at_ibpc.fr>> wrote:
> The cv command is available both in NAMD and VMD, once you've enabled the
> colvars module.
>
> You cannot use Tcl scripting within a colvars configuration file - you can
> use it in the NAMD config file to generate colvars configuration strings as
> in the example I gave above.
>
> Jerome
>
> On 8 September 2017 at 15:44, PRITI ROY <priitii.roy_at_gmail.com<mailto:
> priitii.roy_at_gmail.com>> wrote:
> Dear Jerome,
>
> Thank you for your fast reply. According to your script the "cv" command
> is accesible in vmd as per I know or I might be completely not understand
> well. If possible give some insights.
> I have written one tcl colvar configuration file using four types atom
> index which were saved in ".dat" file and run in loop. But when I run this,
> error shoing that "keyword "set" is not supported". Does "tcl" not
> accessible to colvar?
>
> Kindly enlighten this matter.
>
> Best,
> Priti
>
>
> On Mon, Sep 4, 2017 at 6:10 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:
> jerome.henin_at_ibpc.fr>> wrote:
> Hi Priti,
>
> If I understand you correctly, you want to define a series of 50 dihedral
> restraints. You will need to define one separate colvar for each angle, but
> you don't have to write them separately. That can be scripted using a Tcl
> loop:
>
> for {set i 0} { $i < 50 } {incr i} {
> cv config "colvar { dihedral ... }"
> }
>
> Where the colvar block contains the details of the dihedral angle. You can
> use variable $i inside the block to define the specifics of each angle.
>
> Best,
> Jerome
>
> On 4 September 2017 at 13:08, PRITI ROY <priitii.roy_at_gmail.com<mailto:
> priitii.roy_at_gmail.com>> wrote:
> Dear all,
>
> I would like to do dihedral restrain using the colvar module of nearly 50
> residues. I have gone through the colvar module. In dihedral colvar, there
> are four group selection which are for atoms and depending on 1st group it
> denote the particular dihedral angel. Basically this module describe in
> light of atoms.
>
> How could I define this dihedral colvar for residues?
>
> Please give some idea to resolve my problem.
>
> Thanks,
> Priti
>
>
>
>
>
>
>

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