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

From: Jianwen Jiang <jiangj.che.udel.edu>
Date: Tue, 21 Dec 2004 17:30:47 -0500

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


Ross Walker wrote:

> Dear Jianwen,
>
> Your water residues need to be named either WAT or HOH. If they are not
> called this xleap will think they are a new residue type that it doesn't
> know about. Also, the oxygen atom needs to be name 'O' otherwise xleap will
> think the oxygen is missing and add it.
>
> E.g
>
> HETATM 1444 O HOH 101 17.504 16.825 14.073
> HETATM 1445 O HOH 102 18.877 15.088 18.086
> HETATM 1446 O HOH 103 11.165 21.823 31.513
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of Jianwen Jiang
> > Sent: 20 December 2004 16:19
> > To: amber.scripps.edu
> > Subject: AMBER: use leap to build top & crd files for a pdb
> > file with crytalline water molecules
> >
> > Hi,
> >
> > I started with a pdb file with crystalline water molecules (O atoms
> > only).
> >
> > With the water molecules removed, leap could run successfully to build
> > top & crd files. However, without removing the crytalline water
> > molecules, leap failed. Could some let me know how I can achieve this?
> >
> > Will the command "gwh" or "protonate" help?
> >
> > -
> > Kind regards,
> >
> > Jianwen
> >
>
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Received on Tue Dec 21 2004 - 22:53:00 PST
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