Re: [AMBER] open valence problem

From: Ayesha Fatima <>
Date: Thu, 6 Aug 2020 20:04:23 +0800

Thank you Dr. Case
I try building first. Then i post back.
Thank you again

On Thu, 6 Aug 2020, 8:01 pm David A Case, <> wrote:

> On Thu, Aug 06, 2020, Ayesha Fatima wrote:
> c
> >Thank you for the email. I am posting a picture I snapped in Discovery
> >studio visualiser
> Visualization programs can do odd things with mol2 files. As I said
> earlier, I cannot find any atoms that don't have atom numbers in the
> mol2 file, so I can't tell how you are identifying them. What happens if
> you just type "LoadMol2 bras.mol2" into tleap? (Or use xleap, which will
> visually show you the bonding scheme it is using.)
> I'm not an RED user, so others will have to chime in here. Are you sure
> things are not explained at the RED web page? From the names, it looks
> like
> frcmod.unkonwn are terms that you will have to fill in yourself.
> Don't be afraid to experiment. Use tleap to build a prmtop for just the
> ligand, and run minimization or dynamics on that to see if things look OK.
> ...dac
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Received on Thu Aug 06 2020 - 05:30:02 PDT
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