On Sat, Apr 21, 2012, zhangaidi wrote:
>
> now the error message goes like this :
> Building proper torsion parameters.
> ** No torsion terms for CT-OS-p4-o
> ** No torsion terms for CT-OS-p4-oh
> ** No torsion terms for CT-OS-p4-os
> ** No torsion terms for ho-oh-P-O2
> ** No torsion terms for ho-oh-P-O2
> ** No torsion terms for ho-oh-P-OS
> ** No torsion terms for c3-oh-P-O2
> ** No torsion terms for c3-oh-P-O2
> ** No torsion terms for c3-oh-P-OS
> Building improper torsion parameters.
>
> How shoul I do?
You need to add the force field terms to your frcmod file.
Alternatively, if your modified nucleotide is not much different from one of
the standard nucleotides, asking antechamber to build you a library using
Amber atom types may be an easier way to proceed. You will still need to add
any missing terms in your frcmod file by hand.
There are lots of modified nucleotides here:
http://ozone3.chem.wayne.edu/cgi-bin/login/modi/login/showLoginPage.cgi
Maybe seeing how they work will be of some help to you.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 20 2012 - 13:00:04 PDT
