AMBER Archive (2008)

Subject: AMBER: RE: AMBER Question

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Jul 26 2008 - 08:53:25 CDT

Hi Michael,

My apologies for taking a while to reply, I have been travelling of late. I
am copying this reply to the amber mailing list (amber_at_scripps.edu) which is
the best place to post such questions.

The AMBER force fields typically only support "standard" amino and nucleic
acids. If you have a modified residue such as hydroxyproline then you need
to provide leap with the topology, charges and parameters. There are several
ways to do this, for ligands and things that don't generally look like amino
acids you can use Antechamber and the General Amber (GAFF) force field
(there is a tutorial for this on the amber website). For something that is
just a modified residue then, you could still use GAFF, but it might be
better to modify a similar standard amino acid instead. In this case you
will still need to do a resp fit, decide on the atom types based on analogy
and also add any missing parameters that might be required. Tutorial A1 on
the AMBER website now provides details of how to carry out resp fits
manually, how to build your own units and create frcmod files to provide
missing parameters.

It is also generally a good idea to check if others have created parameters
for such a system previously. For example, the Amber contributed parameters
database contains a number of extra parameter sets:
http://www.pharmacy.manchester.ac.uk/bryce/amber

However, none for hydroxyproline unfortunately. A literature search may show
up some examples you can use.

Good luck,
Ross

> -----Original Message-----
> From: mwentz2_at_ncsu.edu [mailto:mwentz2_at_ncsu.edu]
> Sent: Tuesday, July 22, 2008 9:54 AM
> To: ross_at_rosswalker.co.uk
> Subject: AMBER Question
>
> Dear Dr. Walker,
>
> I was interested in seeing if you had time to help me with a small
> question concerning AMBER. I am trying to use AMBER to analyze a small
> section of collagen with a Hyp-Pro-Gly repeating structure. The problem
> is that anytime I load up xleap to make my topology files, it will not
> recognize the hydroxyproline. I have found by using the list function
> that neither ff03 or glycam 04, which is what I'm using has hydroxyproline
> in it. Is there an easy fix to have hydroxyproline compatible with AMBER?
> And I forgot to mention, I am using AMBER9.
>
> Thank you,
>
> Michael Entz
> North Carolina State University

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