Re: [AMBER] open valence problem

From: Ayesha Fatima <>
Date: Thu, 6 Aug 2020 21:41:56 +0800

Dear Dr. Case.
I built the ligand without issues.
thanks for the advice.

On Thu, Aug 6, 2020 at 8:04 PM Ayesha Fatima <>

> 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 - 07:00:02 PDT
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