VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Mar 05 2022 - 18:33:13 CST

Well, quick test, what happens if you start with whatever your structure
#12 is? Is the problem that particular structure, or the number of
structures? It is very hard for folks on a mailing list to help
troubleshoot a problem that is stated so abstractly, and it would really
help if you put in the time first to come up with a minimal (and shareable)
example that reproduces the problem.
Best,
Peter

On Sat, Mar 5, 2022 at 4:06 PM Mcguire, Kelly <klmcguire_at_ucsd.edu> wrote:

> Hello everyone, I have a script that generates as many PSF and restraint
> files as the user requests, but it gets to structure #12 and then VMD
> crashes with a segmentation fault. The node I'm running it on has more
> than enough RAM. Is there something wrong with my script (see below)? I
> am using VMD 1.9.4a55, is there a bug with Auto PSF? I am closing the
> variables and deleting the molecules each loop iteration, so I don't think
> it's taking up all the memory...
>
>
> for {set i 1} {$i <= $env(b)} {incr i 1} {
>
> package require autopsf
>
> cd ~/$env(a)/Structures/StartingProteinComplexPDBs/
>
>
> #First: Load PDB and Generate PSF with AutoPSF
>
> mol new $env(name)$i.pdb
>
> autopsf -mol top -prefix tompep$i
>
> mol delete all
>
> resetpsf
>
> file rename tompep${i}_formatted_autopsf.pdb ab${i}.pdb
> file rename tompep${i}_formatted_autopsf.psf ab${i}.psf
>
>
>
> #Second: Generate Restraints File
>
> mol new ab$i.pdb
>
> set sel [atomselect top "all"]
>
> $sel set beta 0
>
> set restraints [atomselect top "type C CA N O"]
>
> $restraints set beta 1
>
> cd ~/$env(a)/MinAnnealEquilMD/Structures/
>
> $sel writepdb Minimization_Restraints$i.pdb
>
> mol delete all
>
> $sel delete
>
> $restraints delete
>
> sleep 1
>
> }
>
> quit
>
>
>
> Dr. Kelly McGuire
> Herzik Lab - Postdoc
> Chemistry/Biochemistry Department
> Natural Science Building, 4104A, 4106A, 4017
>