Re: [AMBER] Water models ?

From: Carlos Simmerling <>
Date: Thu, 1 Apr 2010 09:07:49 -0400

look in the manual and archives for the "iwrap" command in sander, and for
postprocessing the "image" command in ptraj.
this is fully expected and normal. it's been discussed often, so it's best
to look in the archives.

2010/4/1 xuemeiwang1103 <>

> Hi :
> Thanks a lot for Case and Carlos's detailed suggestions,I have solved
> the disulfide bonds problem successfully.But now I am puzzeld by another
> problem .I used the TIP3 water model as my explict water model (SolvateBox
> TIP3PBOX) ,I found that the water box is no longer a rectangular box when
> I have done the MD,it looks like a ball,some water molecules even run far
> away from the center,Is this phenomenon normal(the structure of the protein
> seems ok)? Is it better to use the "solvateoct" or other water models to
> aviod this ?Your comments are highly appreciate!
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Thu Apr 01 2010 - 06:30:04 PDT
Custom Search