Re: [AMBER] issues with MMPBSA and explicit waters

From: Jason Swails <>
Date: Tue, 3 Sep 2013 10:59:44 -0400

On Tue, Sep 3, 2013 at 10:09 AM, Alfredo Quevedo <>wrote:

> Dear Jason, thank you very much for you reply.
> I am using Amber12 and the module. I first considered adding
> the parameters of HW to the mdread.F90 file, but I believe that may no
> be the source of the problem, because when I use only one water molecule
> (which also has the HW atom type), the calculation finishes without any
> problem. When retaining 2 o more water molecules this problem arises.
> Also, I think that the missing parameters would also affect calculation
> on the complex, but they seem to crash when the receptor components is
> computed. I checked, and all water molecues are asigned the same atom type.
> To clearly demonstrate the problem yesterday I sent a mail with the
> files attached but they havent been approved by the moderator yet.

Please send them off-list. Large attachments place a burden on the mail
server, and large files should be avoided.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Sep 03 2013 - 08:30:03 PDT
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