AMBER Archive (2009)

Subject: Re: [AMBER] Residues

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Jun 15 2009 - 01:51:56 CDT

Kirtana,

> I made the connections between the residues and then I save them as
> saveoff w7.off
> check w7 gives me following
> Could not find the angle parameters for
> ca-c-c
> ca-c-c
> c-c-os
> c-c-os
> c-c-os
> c-c-os
> Unit is ok
>
> So should I create a separate structure explaning the above angle
> parameters,
> I have the frcmod files of the individual residues and not for the whole
> structure .

You need to add the missing FF parameters in your frcmod file.

If for instance "ca-c-c" is missing, you could use the FF parameters
of "ca-ca-ca" for "ca-c-c".

Or may be Antechamber has some options to do that automatically - if
you want to use gaff.

regards, Francois

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