Re: AW: AW: problem with pdb psf files!

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 04 2012 - 06:15:27 CDT

On Tue, Sep 4, 2012 at 1:06 PM, Jacqueline Schmidt
<jacqueline_schmidt_1983_at_yahoo.com> wrote:
> Dear Norman,
> Can I add my psb/psf files (for the surface+water) to the peptide psf/files
> created by psfgen using the psfgen? If I can do this, it will solve my
> problem.

yes, that should be possible. just split off every segment into separate
pairs of pdb/psf files and then reassemble your system from all of those
segments. there is a plugin trying to automate that process, even.

alternately, you can try using topotools:
http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-mergemols-list-of-molecule-ids-
this is a "closer to the metal" procedure with more flexibility, but also
less checks for errors and inconsistencies.

cheers,
     axel.

> Thanks
> Jackie
>
> ________________________________
> From: Norman Geist <norman.geist_at_uni-greifswald.de>
> To: 'Jacqueline Schmidt' <jacqueline_schmidt_1983_at_yahoo.com>
> Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>
> Sent: Tuesday, September 4, 2012 2:59 AM
> Subject: AW: AW: namd-l: problem with pdb psf files!
>
> Hi,
>
> what is seriously not the problem, is the initial structure as the psf
> doesnít care about coordinates.
>
> So are you sure that your psf contains this improper parameters?
>
> I still donít understand why you donít use your program to build up only the
> initial structure with your molecules as pdb, and just throw it through
> psfgen. Why do you need to create the psf yourself?
>
> As you seem to be familiar with codes, you could check the namd code that
> produces the error, maybe add some debug lines of output, and check what
> namd is reading from your psf. Could you send us a diff output of a psfgen
> generated psf and your own one?
>
> Norman Geist.
>
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> von Jacqueline Schmidt
>
> Gesendet: Montag, 3. September 2012 18:01
> An: Norman Geist
> Cc: namd
> Betreff: Re: AW: namd-l: problem with pdb psf files!
>
>
> 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.
> What is so wired is that the CT1 C O NH1 is always in anypeptide and I
> 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
> to change the writing sequences as in psfgen? thanks again
> Jackie
> ________________________________
> From: Norman Geist <norman.geist_at_uni-greifswald.de>
> To: 'Jacqueline Schmidt' <jacqueline_schmidt_1983_at_yahoo.com>
> Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>
> 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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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
> PARAMETERS FOR CT1 C O NH1
> 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  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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