AMBER Archive (2004)

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

From: Jianwen Jiang (jiangj_at_che.udel.edu)
Date: Wed Dec 22 2004 - 14:01:40 CST

Dear Ross,

Thanks a lot. I get it to work.

Previously, I used leaprc.ff03 force field ("source leaprc.ff03"), and
tleap failed. Instead, now I use "source leaprc.ff99", then tleap works.
All H atoms are added to the crystal water molecules in the same direction.

Jianwen

Ross Walker wrote:

> 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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