Re: AW: problem with pdb psf files!

From: Axel Kohlmeyer (
Date: Mon Sep 03 2012 - 11:20:45 CDT

dear jacqueline,

On Mon, Sep 3, 2012 at 6:01 PM, Jacqueline Schmidt
<> wrote:
> Dear Norman,
> Thanks for your reply. Some of these systems are peptides on the clay
> surfaces that are bound through periodic box in xy directions. I had to
> create the pdb psf files for the surfaces through my own code and then
> added another section to put the peptide on it.
> The question I asked below is for a peptide in solution (as a stating
> point). Vmd loads my pdb psf file with no flaw. All connectivities are
> correct. However namd gives me an error looking for an improper coefficient.

VMD doesn't care about potential parameters.

> What is so wired is that the CT1 C O NH1 is always in any peptide and I

how do you know, did you check?
please load a psfgen generated psf/pdb file combo into VMD
and type the commands:

topo retypeimpropers
topo impropertypenames

that should return a list of all different types of impropers
listed by atom types. you should have something like
CT1-C-O-NH1 among those if it exists.

if you want more details, you can also use:

topo getimproperlist

that should list all improper definitions with the corresponding atom indices.

> really wonder why I get this error while the psfgen generated files wouldn't
> cause this error. Could this be because my structure is for from the
> equilibrium? or it is due to the formatting and I have to rearrange my code

you get this error message, because this specific
improper parameter set doesn't exist in your parameter file.

i suggest you compare a .psf file created for a very small peptide
with your software against what psfgen produces and then have
a closer look at the differences.

> to change the writing sequences as in psfgen? thanks again

the problem looks as if it is more serious that just simple ordering


> Jackie
> ________________________________
> From: Norman Geist <>
> To: 'Jacqueline Schmidt' <>
> Cc: Namd Mailing List <>
> Sent: Monday, September 3, 2012 3:18 AM
> Subject: AW: namd-l: problem with pdb psf files!
> Hi,
> also as a 1st friendly comment, what exactly is the problem when using
> psfgen?
> Are you able to load the pdb/psf pair in vmd? Maybe vmd will tell you
> something.
> Usually md tools must somehow identifiy parts of a structure by some fixed
> properties. I remember that I got some serious problems when I wrote a
> program that had to connect molecules of to pdbs at specific binding sites
> by automatic adjusting and fitting. The problems was about amino acids, that
> had another order than the default is. This caused that I could not identify
> N or C-terminals very comfortable to set the right TER lines there.
> And as I know, NAMD also threats some things about hydrogens hard coded. So
> maybe you also change something that makes it impossible for namd to
> interpret the files correctly. But the developers can maybe tell you more.
> You could check the code of namd, to see what maybe happens, or just stay
> with the order namd seems to expect.
> Norman Geist.
> Von: [] Im Auftrag
> von Jacqueline Schmidt
> Gesendet: Montag, 3. September 2012 04:45
> An: namd
> Betreff: namd-l: problem with pdb psf files!
> Dear Namd users,
> I have got a problem with my pdb/psf file running with NAMD. I have done
> some coding to transfer the car/mdf (insight format) to the pdb/psf file (
> just a friendly first comment: please don't refer me to psfgen because I
> have a surface in my system which can not be dealt with top file)
> When I load the files into the vmd everything seems to be perfect. However
> when I run the files in NAMD I get the error that : CAN'T FIND IMPROPER
> the error message is self explanatory; however, I don't understand why I am
> getting this error at all, because the indicated atom types are the backbone
> atoms which every FF parameters should be already in the parm file.
> The only difference between my pdb psf files is that I write the
> non-hydrogen atoms in any residue first followed by the list of hydrogen
> names/ff-types. Is this a problem??
> As a test I made the pdb/psf files with psfgen too. Everything between the
> files is again the same except two things 1) the order of the atoms 2) It
> does not include the right c-terminal atoms with their FF-type indicated in
> the top file. I simply treats the last carbon as C C (name and FF-type)
> instead of C CC and only one oxygen at the end which is O O instead of OT1
> OC, and the OT2 is not in the file at all (it was in my original pdb that
> feeded into the psfgen though).
> I hope someone can help me please, I am really confused
> jackie

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:30 CST