AMBER Archive (2008)

Subject: AW: AMBER: tleap and Zn parameter

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Tue Sep 02 2008 - 01:46:23 CDT

Hello David,
Thank you very much for your answer and sorry for my to short error
description.
Here comes a more detailed error message:
when I use desc zn, then is the following output:
UNIT name:
Head atom: null
Tail atom: null
Contents:
R<ZNA 363>

I think, here is the mistake, the ZNA.lib is not completly imported.
I proved the pdb, here is ZNA as atomtype and it is the correct numer
(363)and also in correct columns, but the ZNA.lib is a little bit longer.
Do I have a change, when I try to install the xleap (here where some
installing problems with the AmberTools) and edit the zna.lib in xleap again?
When I load my pdb after loading zna.lib and frcmod.zna I get following error
message:
> test=loadpdb "test.pdb"
Loading PDB file: ./test.pdb
Unknown residue: ZNA number: 331 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
  Added missing heavy atom: .R<NME 362>.A<CH3 3>
Creating new UNIT for residue: ZNA sequence: 363
Created a new atom named: ZNA within residue: .R<ZNA 363>
  total atoms in file: 2657
  Leap added 2579 missing atoms according to residue templates:
       1 Heavy
       2578 H / lone pairs
  The file contained 1 atoms not in residue templates

After that, no prmtop and inpcrd could write out.
I hope, these informations helps you to find out, what my problem is.
Have a nice day!
Susanne

-----Ursprüngliche Nachricht-----
Von: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]Im Auftrag
von David A. Case
Gesendet: 01 September 2008 15:53
An: amber_at_scripps.edu
Betreff: Re: AMBER: tleap and Zn parameter

On Mon, Sep 01, 2008, Aust, Susanne wrote:
> I create with Amber 7.0 (xleap, ff99) a zna.lib and frcmod.zna for my zinc
> ion and it works.

> Now I have Amber 10.0 and use tleap with ff03 and try to do the same
before.
> tleap load both old files correctly.
> But when I load my pdb, the program could`nt use my zna.lib and so I
could`nt
> generate a prmtop and inpcrd.

We will need more information to be of any help here. After you load
the zna.lib file, use the list and desc commands to check that the zinc
parameters are what they should be, and that they match what is in the
pdb file. Be sure the atom and residue names in the pdb file are in the
correct columns: recent code may be more strict than before for.

If that doesn't work, please give the input commands you used, and the
exact error message (more than just "the program couldn't use my
zna.lib"), plus other relevant information.

...good luck...dac

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