AMBER Archive (2005)

Subject: AMBER: Problems with parameter lib and prep püarameter files

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Mon Jul 04 2005 - 04:14:56 CDT

Dear Amberians, dear Ross,

thanks for your friendly answer on my last eMail.

I tried to use the NAD+ parameter files by Walker on
http://pharmacy.man.ac.uk/amber/.

To use these parameters I added the following lines to my leaprc :

frcmod_nad+ = loadamberparams frcmod.NAD+
loadOff NAD+.lib

After loading a single NADH into xleap I got the output below.

If I open the structure with "edit a" I get the editor with
two strucures within. First I get a well connected NADH molecule
which looks fine and in addition the the molecule but as a bunch of non
connected
single atoms.

Do I somehow add the parameter files the wrong way ?

What else could be wrong ?

Best regards,

Daniel Wetzler

P.S. : My xleap output :

Welcome to LEaP!
Sourcing leaprc: ./leaprc
Log file: ./leap.log
Loading Prep file: ./nad+.prep
Warning: per-line charges being overridden by CHARGE block in NAD+,
AMBER 5.0 compatible; U. Ryde, to be published, 22/4-98
Loading parameters: ./frcmod.NAD+
Reading force field mod type file (frcmod)
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
Loading library: ./NAD+.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib
Loading parameters: /usr/local/amber7/dat/leap/parm/parm94.dat
Loading parameters: /usr/local/amber7/dat/leap/parm/gaff.dat
> a = loadPDB "/home/daw/Desktop/jan_projekt/nad_jan.pdb"
Loading PDB file: /home/daw/Desktop/jan_projekt/nad_jan.pdb
Created a new atom named: N6 within residue: .R<NAD 0>

Created a new atom .............. and so on

.....

total atoms in file: 44
  Leap added 70 missing atoms according to residue templates:
       44 Heavy
       26 H / lone pairs
  The file contained 44 atoms not in residue templates
> edit a
> Welcome to LEaP!
ERROR: parse error

> Sourcing leaprc: ./leaprc
ERROR: parse error

> Log file: ./leap.log
ERROR: parse error

> Loading Prep file: ./nad+.prep
ERROR: parse error

> Warning: per-line charges being overridden by CHARGE block in NAD+,
AMBER 5.0 compatible; U. Ryde, to be published, 22/4-98
ERROR: parse error

> Loading parameters: ./frcmod.NAD+
ERROR: parse error

> Reading force field mod type file (frcmod)
ERROR: parse error

> Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
ERROR: parse error

> Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
ERROR: parse error

> Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
ERROR: parse error

> Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
ERROR: parse error

> Loading library: ./NAD+.lib
ERROR: parse error

> Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
ERROR: parse error

> Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib

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