AMBER Archive (2007)

Subject: Re: AMBER:

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jun 08 2007 - 13:47:43 CDT

welcome to Amber!

1) don't use parm99 unless you are sure you want all of its problems.
I recommend ff99SB, check the archives for details.

2) copy error messages in the email so we can see the problem.
does the protein have anything other than amino acids?

On 6/8/07, Taryn Hartley <taryn_hartley_at_hotmail.com> wrote:
>
> I am a new-to-Amber user and after completing the tutorials, am attempting
> to work with some molecules pertaining to my research. In loading and
> attempting to save .inpcrd and .prmtop files using xLeap (with force field
> 99, leaprc.ff99) I am recieving "FATAL" error messages, saying that some
> of my atoms don't have atom types. The molecules I am using are directly
> from the Protein Data Bank with no modifications. Has anyone else confronted
> this problem? If so, what solution did you find works best?
>
>
> Thanks in advance,
>
> Taryn
>
> ------------------------------
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