Re: [AMBER] Boron compunds with "pdb" file with novel frcmod file

From: David A Case <>
Date: Sun, 15 Mar 2020 12:41:26 -0400

On Sat, Mar 14, 2020, Erdem Yeler wrote:

>I parameterized boron and I created my *.frcmod file, for mol2 files,
>everything was OK. I heated my molecule, calculated RMSD, minimized and
>found very very close X-ray structure, I also calculated resp charges
>exc.... exc... But yesterday I tried to run MMPSA for DNA-boron compund

It's hard to reply here, but I'll try to be as clear as possible. It
doesn't look like your problems are related to boron, but rather to
combining a small molecule with DNA.

It appears that you can run MD simualtions on the small molecule, but
are having troubles with the DNA-boron complex.

>1) I had to turn my bor.mol2 file to bor.pdb pdb file because I had to
>use DNA.OL15 force filed too

You will need to create a combined PDB file with the DNA and the small
molecule placed in the correct place, that is docked into place. Many
programs convert a mol2 file to pdb, including antehchamber:

   antechamber -fi mol2 -i resp.mol2 -fo pdb -o ligand.pdb

You can create the combined pdb file either with a docking program or
with a visualization program; or maybe(?) you already have a starting
structure of the DNA + ligand that you can use.
> sander -O -i -o min.out -p x.prmtop -c x.inpcrd -r min1.ncrst

As best I can tell from your email (and maybe I missed something here),
the "x.prtmop" file just has the small molecule. That is, I didn't see
anything that involved tell tleap about the DNA. But you've already
said that you were successful in running the small molecule by itself,
which leads to my confusion.

>I didn't get any error message but mdin file said:"nothing" :)

I don't follow you here.

>So I checked what happened and here is what I got :
>ambpdb -p x.prmtop -c min1.ncrst > pdb.pdb

It sounds like there is indeed a problem with the x.prmtop file, but see
above for things you might look for. If the "resp.pdb" file that you
loaded indeed has DNA in it, be sure that there is a TER card between
each DNA chain, and between DNA and ligand.

Basically we need to know what is in the PDB file you loaded into tleap.


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Received on Sun Mar 15 2020 - 10:00:02 PDT
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