AMBER Archive (2004)

Subject: RE: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Dec 21 2004 - 23:26:48 CST

Hi Jianwen,

Works fine for me:

>xleap -s -f /usr/local/amber8/dat/leap/cmd/leaprc.ff99

Welcome to LEaP!
Sourcing: /usr/local/amber9/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /usr/local/amber8/dat/leap/parm/parm99.dat
Loading library: /usr/local/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber8/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber8/dat/leap/lib/solvents.lib
> test=loadpdb 1AKI_wat.prb
Could not open file 1AKI_wat.prb: not found
> test=loadpdb 1AKI_wat.pdb
Loading PDB file: ./1AKI_wat.pdb
  total atoms in file: 1079
  Leap added 1115 missing atoms according to residue templates:
       1115 H / lone pairs

(Works fine with tleap as well)

What is the error message you see?

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |
 

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Jianwen Jiang
> Sent: 21 December 2004 14:31
> To: amber_at_scripps.edu
> Cc: Ross Walker
> Subject: Re: AMBER: use leap to build top & crd files for a
> pdb file with crytalline water molecules
>
> Dear Ross,
>
> Thank you for your suggestion. In fact, I did exactly what
> you said, but not
> successfully. Attached please find two pdb files I have
> tried, which were
> modified from 1AKI.pdb from RCSB database by changing CYS to
> CYX; one file
> (1AKI_wat.pdb) with the crystalline water molecules and the other
> (1AKI_nowat.pdb) with water molecules removed. Then tleap
> (version 7 or 8) was
> used to build toplogy, successfully for 1AKI_nowat.pdb, but not for
> 1AKI_wat.pdb.
>
> Because xleap does not run in my computer, I am not sure
> whether it will make
> difference if xleap is used. Please help me to check it out.
> Thanks for the
> help.
>
> Jianwen
>

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