From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Tue Feb 26 2013 - 16:17:34 CST
To my knowledge autopsf will not generate an additional new molecule (like
a protein or the like)
did you load just a pdb file into VMD and used autopsf?
In this case your pdb most probably does contain already the "mistake".
Some structures from the PDB may contain multiple conformations of one
molecule for which most of the atoms are identical. Maybe that is the
reason. In any case, since you know which molecules are duplicate, you have
to get rid of one of the molecules. You can load the pdb file in question
into VMD, select what you wanna keep, and then write this selection (e.g.
with writepdb command) into a new pdb file which you will use to build your
P.S.: I noticed, we sent the mails off list, so I put it back to the list
On Tue, Feb 26, 2013 at 10:45 PM, Patricia Campbell <
> Hello Eddi,
> You are right. I checked my psf/pdb files and there are two molecules
> right on top of each other. I have been using the autopsf function in VMD.
> How can I get around this error? Thank you so much for your response.
> On Tue, Feb 26, 2013 at 4:32 PM, Eduard Schreiner <
> eduard.schreiner_at_gmail.com> wrote:
>> Hi Patricia,
>> you may wanna check your psf/pdb files you are using for the simulation
>> one more time. It sounds like you may have multiple copies of the same
>> molecule in there, i.e. there may be two or more molecules (your monomers)
>> right on top of each other. I had once a similar experience, which was due
>> to a mistake in my psfgen script.
>> On Tue, Feb 26, 2013 at 10:01 PM, Patricia Campbell <
>> patricia.campbellsoup_at_gmail.com> wrote:
>>> I am trying to run a large simulation comprised of over 20 monomers (1.6
>>> million atoms total after solvation/ionization). The simulation never makes
>>> it past the first step of equilibration before crashing due to atom
>>> velocity. Recently, I tried running the structure through 20000
>>> minimization steps. I checked the structure and I noticed that the dcd file
>>> adds a monomer on top of another monomer after the first frame. When the
>>> equilibration crashes its due to atoms located in either of these two
>>> monomers. The two monomers are right on top of one another. I have no idea
>>> how this is happening. I also tried running a minimization in vacuo and the
>>> same thing happened after the first frame. Furthermore, I tried deleting
>>> the second monomer out of the PDB file but then was unable to load the PDB
>>> file into the PSF file in VMD. Is there any way to stop this??? Thank you. I
>>> have to add that when I run this simulation on 6 monomers or less this does
>>> not happen. I need to run this larger scale simulation so that I can
>>> monitor interactions between hexamers and pentamers (this is a part of a
>>> capsid). Thank you.
>>> Patricia Campbell
>>> Patricia Campbell
> Patricia Campbell
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