Re: [AMBER] pdb to mol2 conversion via antechamber

From: Liao <>
Date: Fri, 17 Jan 2020 02:20:02 -0600

If this is a natural DNA and you just want to run MD on it, you don’t need to do any conversion or parametrization. Just load it as a pdb. Parmchk is suppose to return you an empty file in that case.

If this is an artificially modified DNA then it can take some work to get it ready-not something a few sentences can cover. But if you know about prep files, then the direction is to convert the DNA into prep file residues, the same way protein and DNA information is stored in the AMBER library. There is an example prep file template stored in your installation, and there is also the “prepgen“ command, which there should be somewhat detailed descriptions on it in the AMBER manual.

Sent from my iPhone

> On Jan 17, 2020, at 12:23 AM, Sruthi Sudhakar <> wrote:
> Hello everyone,
> I have been trying to convert a DNA structure in pdb format to mol2 via
> antechamber, so that I can run parmchk2 command on the same. But when I run
> antechamber I get error message and the conversion doesn't get completed.
> It says the number of atoms exceed the MAXATOM.
> I also get a message to use the following command for conversion:
> antechamber -j 5 -at sybyl -dr no
> But I am not familiar with this command.
> So please suggest any way to convert the file so that I can run the
> parmchk2.
> Thanking you all in advance.
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Received on Fri Jan 17 2020 - 00:30:01 PST
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