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 - 01:53:00 PST
