Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer

From: Lod King <>
Date: Sat, 16 May 2020 13:16:25 -0700

It is in pdb format, I also have it with mol2 format. I am sure that the
CONECT recorded.

I do not think it is about the Hydrogens issue. As Furazan molecule has One
O and Two Ns in a five-membere ring, and it had the same error.

Note that it worked when I use pdb format instead of mol2 format, although
I often use mol2 file to generate my prepc and frcmod files.

But I will also test using '-dr no' and see.

On Sat, May 16, 2020 at 5:05 AM David A Case <> wrote:

> On Fri, May 15, 2020, Lod King wrote:
> >
> >I got the following error when using $antechamber to generate prepc and
> >frcmod files
> It would be important to see the input file you used. Is it in pdb or
> mol2 format (or something else)? If in pdb format, does it have CONECT
> records? Are you sure those are correct?
> >Weird atomic valence (3) for atom (ID: 7, Name: O).
> > Please check atomic connectivity.
> >
> >how should I fix it? my O is connected by two Ns in a five-member ring,
> btw.
> If you are convinced that everything is OK, and all hydrogens are
> present, you can add '-dr no' to turn off the acdoctor checks. But then
> be specially careful to check the output to make sure it makes sense.
> ...dac
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Received on Sat May 16 2020 - 13:30:02 PDT
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