AMBER Archive (2009)

Subject: Re: [AMBER] leap and chirality

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Tue Mar 24 2009 - 03:11:38 CDT

Hi Wei,

        Thank you for the prompt reply and patch. I applied the patch and corrected
the two prep files. sleap successfully ran without giving errors, and it
provides pdb files with the correct chirality.

        However two more problems arose. First, the connection table appears to be
incorrect in the sleap generated pdb. If you load the pdb into vmd/rasmol/etc
it provides incorrect bonding patterns. Manually removing the connection
table provides the correct bonding pattern.

        Second, if I extend the molecules to include 4 residues instead of two, using
the command "a = sequence { BBB BBB AAA AAA }", TER statements are introduced
after the 2nd and 3rd residues.

        On a different note, when I try to use my own leaprc and force_field.dat
files, which have worked for amber8 and amber9 leap, I obtain the following
error message:
"Error: can not find atom 1 in molecule."
This error occurs without loading any prep files or molecules - just my leaprc
and the force_field.dat file.

Thanks,
Karl

On Monday 23 March 2009 19:36, Wei Zhang wrote:
> Hi Karl,
>
> Can you apply the patch I attached and try sleap again?
>
> NOTE, there is a minor problem with your prep file. There are two
> atom with the
> same name "H8", you might want to change one of them to some other
> name say "H10".
>
>
> Sincerely,
>
> Wei




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