AMBER Archive (2008)

Subject: Re: AMBER: Topology file format for Amber9

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 23 2008 - 11:01:13 CDT

On Wed, Apr 23, 2008, Xioling Chuang wrote:
>
> I found that in "http://amber.scripps.edu/formats.html" the parameters
> are in the format (12i6), total 30 parameters starting from NATOM to
> IFCAP. However, the prmtop file provided by amber9 consists of 31 parameters
> with the format (12i8). So, I think that the format in the website above
> should not for AMBER9. Could anyone let me khow where I can find the prmtop
> file format for AMBER9?

For now, the source code is your best hope, (look at rdparm.f in sander or
prm.c in NAB) although the differences with the older format are small, and
you can probably figure out most things from what is on the web page.

Volunteers to update the file formats page are hereby solicited. (I'm always
hoping that some student or post-doc in one of the Amber developers' groups
will step forward and help out, but it rarely seems to happen.)

...regards...dac

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