AMBER Archive (2008)

Subject: Re: AMBER: Prepgen

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu May 15 2008 - 10:46:34 CDT

Hi Ojha,
Could you send me your input file and mainchain.dat file? I would like to
figure out what the problem is.

Best

Junmei

On Wed, May 14, 2008 at 4:45 AM, Rajendra P. OJHA <rp_ojha_at_yahoo.com> wrote:

> Dear Professor Ross Walker,
> We are not able to create the parameter for new
> molecules. As mentioned in the program some additional
> atoms were added at both ends to calculate the
> potential from G03. But, when machine.dat file was
> used to calculate the charges at the atomic centers.
> It gives the same charges which were in the original
> molecule. As a result of which the total charge on the
> molecular system is not zero, which was mentioned in
> the machine.dat file.
> I send it on AMBER net but we have not yet
> received any reply.
> Please rectify the problem and suggest what to
> do.
> Thank you very much and with regards,
> Ojha
>
>
>
>
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