[AMBER] open valence problem

From: Ayesha Fatima <ayeshafatima.69.gmail.com>
Date: Tue, 4 Aug 2020 22:34:19 +0800

Dear all,
I would like to prepare the cholesterol molecule as ligand for md
simulation. previously I docked the molecule into a protein to get a
complex. I extracted it and prepared a charged mol2 file using the PyRED
server. now that want to convert to the mol2 to be used in the amber I
cannot generate the mol2 file. I opened the file in notepad and can see
that a terminal C and terminal OH atom has no atom numbers. The error
message says "Weird atomic valence (3) for atom (ID: 34, Name: C14).
Possible open valence." C14 in the structure is attached to another

Could anyone guide with the correct method to prepare the ligand file?
do i need to use the antechamber after the using the PyRED server?

I am attaching the files for reference. bras.mol2 is the PyRED generated
mol2 file and Mol_red.pdb.pdb is the originally submitted file

I am using amber18 with ambertools19

Thank you
Ayesha Fatima

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Received on Tue Aug 04 2020 - 08:00:02 PDT
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