AMBER Archive (2007)

Subject: Re: AMBER: using glycam04 parameters

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 18 2007 - 10:28:27 CDT

On Wed, Apr 18, 2007, Sara Alexandra Moura wrote:

> I have used that site, but I need to use Xleap to solvate the system, and it
> does not recognize the C1-OH, even when created by that site. What is
> the point
> of having a carbohydrates parameters set, if I have to compute parameters
> for
> the C1-OH linkage, it makes no sense!
> I'm really frustrated...

So am I: I asked if you would tell us exactly what commands you used in LEaP,
but I don't think I saw them. Your problem could have all kinds of origins:
missing parameters in glycam, a bug in LEaP, operator error, bad
documentation, etc. Several people on the list have tried to help. Now you
have to do your part.

...dac

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