VMD-L Mailing List

From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Mon Mar 07 2022 - 13:15:35 CST

Should also mention our cluster uses Ubuntu 18.04.6 LTS if that helps...

Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017
________________________________
From: Mcguire, Kelly <klmcguire_at_UCSD.EDU>
Sent: Monday, March 7, 2022 10:23 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: PSF Script

I even tried adding psfcontext new delete after the resetpsf by another person's suggestion, but it still crashes...

Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017
________________________________
From: Mcguire, Kelly <klmcguire_at_UCSD.EDU>
Sent: Monday, March 7, 2022 10:21 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: PSF Script

Still haven't found a solution to the segmentation fault when trying to create lots of psf files in Linux VMD 1.9.4a55 text mode using autopsf on our Linux cluster.

Here are 20 of the structures and the AutoPSFScript.vmd that I run. Doesn't matter which 13 you try to run, it will crash, at least with the VMD 1.9.4a55 on our cluster. I create a directory called TOM70Pep_12 in my home directory. In that TOM directory I have TOM70Pep_12/Structures/StartingProteinComplexPDBs/{20 structure files placed here}. Also, in TOM70 directory, I have another folder called Scripts. TOM70Pep_12/Scripts/{AutoPSFScript.vmd placed here}. I tried 1 to 13, or 8 to 20 and it still crashes with the segmentation fault when it hits the 13th structure.

Any ideas on

Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017
________________________________
From: Mcguire, Kelly
Sent: Saturday, March 5, 2022 9:50 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: PSF Script

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