Dear Professor Case,
Thank you for your advice.
>Why do you need a prepin file in this case? Can't you use the mol2 file,
I need the PREPIN file to use unusual type residue in substrate molecule.
After QM calculation of the residue with caps by ACE and NME,
I converted Gaussian log-file into MOL2 format file.
Then the MOL2 file was used to AC file.
I recognized that the coordinates and connection information is
Same as those of MOL2 files.
So, the problem is the final Prepin file does wrong connection,
Although the MOL2 file has right one.
> maybe setting the head and tail atoms by hand?
Can I think that I can add "head and tail" information in MOL2 file
Before conversion into AC file?
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: case [mailto:case.biomaps.rutgers.edu]
Sent: Monday, February 11, 2013 2:44 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN
On Sun, Feb 10, 2013, kurisaki wrote:
>
>
> However, the PREPIN file generated by RESIDUEGEN module
> possess wrong Topology, I mean, main chain atoms were
> mistakenly assigned and atoms for loop had alternative bond.
>
> p.s. I consider that MOL2 file is right;
> it has proper connection.
Why do you need a prepin file in this case? Can't you use the mol2 file,
maybe setting the head and tail atoms by hand?
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 10 2013 - 20:00:02 PST
