Subject: Summary: Tinker outputs

From: Kiss Gergo <[email-masked]>
Date: Thu, 27 Nov 1997 18:52:28 +0100 (MET)

Hi everybody,

I posted this question some days ago to the list:

>I use the Tinker package for some calculations on peptides. The problem
>is, that the output is in Tinker's xyz format. Rasmol, Molmol and Molden 
>can't read this. If I use the included xyzpdb.x program for converting to
>pdb, Rasmol and Molden reads the file, but none of them can perform
>backbone calculations.
>Do you know about a graphical software, which can read Tinker's xyz
>format, or about a converter, which can turn this file into usable form.
>Please help me, I will summarize the answers.
>
The answers I got:

1.-----------------------------------------------------------------------

Hi,

My gOpenMol program can read both Tinker single coordinate and multi
coordinate files. The release 1.0 (with the Tinker reader) is will be
ready in a few days.

Address:

http://laaksonen.csc.fi/gopenmol/

Regards,

-leif laaksonen

2.--------------------------------------------------------------------

Dear Gergo Kiss,

      If your molecule is a peptide/protein, then xyzpdb should write
 a PDB file that is "correct" in all respects and will be able to do
 backbone calculations, etc. in Rasmol, and so on. In order for the
 correct PDB file to be created by xyzpdb, you must have a TINKER
 sequence file (.seq file) present during the conversion process so that
 xyzpdb will know it is dealing with a protein and will correctly parse
 the xyz file looking for the correct sequence of amino acids. The
 sequence file is created automatically by the pdbxyz program whenever
 a PDB file is translated to xyz format, and also when the protein program
 is used to build an arbitrary structure from a sequence and set of
 phi-psi-chi angles. If the sequence file is not present during xyzpdb,
 then the program will assume that your system is nonpeptide and will
 write a PDB file that follows the PDB format, but does not use standard
 residue names, atom names and such that Rasmol and other programs expect.
 The recent version of TINKER should be able to handle xyz <--> PDB
 conversions for multiple chains of peptide/protein optionally followed
 at the bottom of the file by water molecules and/or ligands. We have
 recently added the ability to handle a limited selection of "capping
 residues" for the polypeptide chains. This last feature will be added to
 the distribution version on http://dasher.wustl.edu/tinker/ shortly.

      In addition, you might look into the Babel software. This is a
 public domain molecule file format converter. While I have not yet done
 so, it should be a fairly simple matter to write a TINKER module for
 Bable that will allow conversion of TINKER xyz to/from PDB and other
 formats.

      Hope this helps.

                          Best wishes, Jay Ponder

3.-----------------------------------------------------------------------

Dear Kiss Gergo,

About molden. First there is already a tinker xyz routine in molden,
but it is only accessible from the z-matrix editor mapxyz/optimise option.
I will add a commandline flag to force tinker xyz reading.
But still there is a way to accomplish what you want in molden:

- use the xyzpdb.x program for converting to pdb

- start molden with the -f commandline flag.

Regards, Gijs

-------------------------------------------------------------------------

So these were the answers. My problem was that I didn't have the .seq file
in the working directory. Copying it there helped the problem.

Grateful thanks for everybody who sent me suggestions.

I hop this summary will help some of you in using Tinker, which is a very
powerful software package.

Kiss, Gergo
[email-masked]