Re: [AMBER] problem during TMD simulation

From: Simon Becker <>
Date: Mon, 13 Dec 2010 10:23:48 +0100

Hi Dachuan,

the recommended way is to play with the box parameters until you find a
box with the correct amount of water.
However, opening the reference inpcrd file with an editor and removing
the desired amount of coordinates worked fine for me. Do not use this
edited file as input for simulation (-c) only for reference (-ref).


Am 12/13/2010 09:45 AM, schrieb Dachuan Guo:
> Amber users,
> I have two protein structures A/B with the same sequence. I want
> to use TMD to simulate the process from A to B. When I used
> "solvateoct *** TIP3PBOX 9.0", there were different number of residues
> added to system A and B. TMD can't run without the same number of
> atoms.
> How could I add the same number of water into the two protein systems?
> regards,
> Dachuan Guo

Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647 Universitaet Konstanz
D-78457 Konstanz
Tel: 0049 7531 882900, Fax: 3183
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Received on Mon Dec 13 2010 - 01:30:03 PST
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