Re: test and a short question!

From: Fangqiang Zhu (
Date: Mon Jan 19 2004 - 15:15:15 CST


Yes, I think this problem was solved in the newest (current) version of
NAMD by Jim. So now you can directly use your original parm file (as
would be used in Amber) without any change.

We'll update the user's guide accordingly in the next release of NAMD.


Vlad Cojocaru wrote:

> Dear NAMD users,
> Hello from a new member of this very welcomed list. I just have a
> short question:
> There was a problem with the TIP3 water from Amber in NAMD in the sense
> that the angle H-O-H was not restrained (even when rigidbonds all was
> used). A solution for this problem was given to me by amber people which
> suggested to change the topology file for water in such a way that in
> does not contain a H-H bond but rather an H-O-H angle. This worked fine
> for me so far and the problem was fixed for earier versions of NAMD.
> The disadvantage was that I was using different topology files when
> running Amber and Namd
> I noticed that the 2.5 version this problem does not exist anymore.
> Although the output still warns about the H-H bond the angle H-O-H is
> maintained during simulation.
> My question is: Is the problem solved now and which was the last NAMD
> version which still had this problem?
> Thank you very much and I am looking forward to very interesting
> subjects on this mailing list
> Best regards
> Vlad Cojocaru
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail:
> home tel: ++49-551-9963204

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