From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Sat Mar 05 2022 - 11:50:08 CST

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


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



Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017