Re: Atoms moving too fast OR constraint failure in RATTLE algorithm

From: Diego Alejandro Vargas (
Date: Sat Nov 08 2008 - 17:31:30 CST

I had not noticed those problems in the .psf files. How did you catch that?
Just by looking at the structure in vmd?

Anyway, thanks again. I have been looking at the different pdb and psf files
for the protein at each step (generating psf, solvation, etc.). You are
right, there is a problem with the structure (psf) files.

The pdb files look normal in vmd, it is when the psf file is loaded as well
that those long bonds start to show.

Originally I had tried to make the psf files with the automatic psf
generator in VMD, but I couldn't (I tried today again and was able to do so.
The psf files look better: I am going to try and run the simulation again
with these new files, see what happens).

But those I created for the simulation you are looking at I did by:

The original pdb file for the protein was given to me by a professor. He
told me he generated the structure through the program Swiss-prot. Following
the tutorial I generated the psf through the psfgen package in TK console in

* package require psfgen topology top_all27_prot_lipid.inp pdbalias
residue HIS HSE pdbalias atom ILE CD1 CD segment U {pdb
ser39alap.pdb} coordpdb
ser39alap.pdb U guesscoord writepdb ser39ala.pdb writepsf ser39ala.psf
*Some warnings encountered for some of the commands:
* segment U {pdb wt_fascin.pdb}*
Info: skipping improper N-C-CA-HN at beginning of segment, cross-term, bond,
and conformation at end of segment, etc.

*coordpdb wt_fascin.pdb
*Warning: failed to set coordinate for atom...
(obtained for 2 atoms)
Warning: poorly guessed coordinate for atom...
(obtained for 9 atoms)

*Next I solvated the protein thorugh solvate package with 20 Angstrom of
water in each dimension past outmost atom of protein.

*I don't know how different the autopsfgen and this script are and how much
do these warnings matter, but the files look better now.

I did not add ions to structure because I think the protein is charged and
there is no need. My professor said this was fine (but he is not a NAMD
user, so correct me if I'm wrong).

With respect to the .log files. I don't know why no log files are generated.
The minimization simulation ends successfully, and both .coor, .vel, and
restart files are created, but no log files. I looked in the manual see if
there was a command, but found none. I thought it should always be
generated. I searched in the discussion board but found nothing on this. Any
idea of why?

Finally, I'm attaching the .xst files for both minimization and
equilibration (ser39ala_wb_mn.xst and ser39ala_wb_eq.xst respectively). I
believe you already have all the input pdb and psf files.

Thank you for your patience. Let me know if you need anything else or if you
would rather wait until I tell you how the simulations with the new psf
files go before looking more into this.


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