AMBER Archive (2000)

Subject: partial solvation

From: EOIN GALLIGAN (paxeg_at_pan1.pharm.nottingham.ac.uk)
Date: Fri Sep 08 2000 - 05:56:30 CDT

Dear All,
I am having trouble adding a solvent cap to a
protein - ligand system. I wanted to center the
cap at the end termini of the ligand. To check
the coordinates i used the desc command.
Then, I used
solvatecap unit WATBOX216 { x y z } r

where x,y and z are the location of the end
termini of the ligand,and r is the radius.

However, the sphere appears far away from the
system and NOT at the location I specified. Any
ideas why this has occurred??

Regards, Eoin Galligan
Graduate Research Student
Laboratory of Biophysics and Surface Analysis
Institute of Pharmaceutical Sciences
University of Nottingham
Nottingham
TEL: 00 44 (0)115 9515151 x66272
MOB: 00 44 (0)7968 349629
MOB MAIL:eoingalligan_at_sms.genie.co.uk

Laboratory of Biophysics and Surface Analysis,
Institute of Pharmaceutical Sciences,
University of Nottingham,
Nottingham
UK