Re: [AMBER] open valence problem

From: David A Case <>
Date: Tue, 4 Aug 2020 21:44:32 -0400

On Tue, Aug 04, 2020, Ayesha Fatima wrote:

>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.

I don't see any such atoms with no atom numbers in the "bras.mol2" file that
you attached. Can you be more specific about what you found confusing about
the mol2 file. I looked at the structure in Chimera, and didn't see any
problems -- but it's a sizable molecule, and I might have missed something.

> 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

Can you give the exact command and input files you used to get this message?

>do i need to use the antechamber after the using the PyRED server?

Did pyRED provide a frcmod file to go along with the mol2 file? If so, you
should be ready for tleap. If not, you may need to run parmchk2, but you
should not need to run antechamber itself.


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Received on Tue Aug 04 2020 - 19:00:03 PDT
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