Dear sir,
Thank you, I was trying to use pdb4amber on docked (reduced) ligand.
pdb4amber -i lig_h.pdb -o lig_reduced.pdb --reduce
This was removing the connect record from the pdb file. This was causing
the sqm to lay a penalty score on few of the bonds.
I am guessing another reason for this is because of the docking program
introducing torsions in the ligand while it is guessing, the best pose for
complex formation.
I could overcome the problem by omitting the step mentioned above.
Thank you,
regards.
On Fri, Jul 5, 2019 at 10:38 PM Prasanth G, Research Scholar <
prasanthghanta.sssihl.edu.in> wrote:
> Dear all,
>
> I had docked mefenamic acid with a proteinand followed the sustiva
> tutorial for obtaining frcmod file. which reads as follows:
> ---------
> Remark line goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> ca-ca-nh-hn 1.1 180.0 2.0 Same as X -X
> -na-hn, penalty score= 41.2 (use general term))
> ca-ca-ca-nh 1.1 180.0 2.0 Using the
> default value
> ca-ca-ca-ha 1.1 180.0 2.0 Using general
> improper torsional angle X- X-ca-ha, penalty score= 6.0)
> c -ca-ca-ca 1.1 180.0 2.0 Using the
> default value
> ca-o -c -oh 10.5 180.0 2.0 Same as X -X
> -c -o , penalty score= 24.5 (use general term))
>
> NONBON
> ------
>
> Can someone please indicate if it is an acceptable penalty score..?
> I am attaching the pdb file for your reference
> Thank you in advance.
>
> --
> Regards
>
>
> Mef_reduced.pdb
> <https://drive.google.com/a/sssihl.edu.in/file/d/1csULhX8Ydntdo9xmzC3I6jMY3q7pFbdT/view?usp=drive_web>
>
--
Regards,
Prasanth.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 10 2019 - 10:00:03 PDT
