AMBER Archive (2009)

Subject: Re: [AMBER] leap and chirality

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Tue Mar 24 2009 - 07:55:47 CDT

Hi Karl,

     Thank you for the information. The first two errors are familiar
to me,
I think I know what the problem might be. As for the last one, can you
send me your force_field.dat and leaprc?

     Sincerely,

     Wei

On Mar 24, 2009, at 3:11 AM, Karl Kirschner wrote:

> 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
> <
> res_a.prep><res_b.prep>_______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber