Re: [AMBER] Nucleic residues with methylphosphonates

From: FyD <>
Date: Fri, 17 Jun 2011 07:37:40 +0200

Dear Sasha,

You could use R.E.D. Server
This server will provide the hardware & software to derive RESP or ESP
charges and generate force field libraries. R.E.D. Server is open to
all; you only need to register if you want to use Gaussian 2003/2009.

1) You prepare the PDB files by using builder of R.E.D. Server

2) You run R.E.D. Server/Ante_R.E.D. 2.0 to generate the P2N files
from the PDB files

3) You run R.E.D. Server/R.E.D. IV to generate the mol2 files from the
P2N files

You might look at R.E.DD.B. as well; The project of Lei Tao as an example.

regards, Francois

> I am attempting to use AMBER to simulate DNA with some neutralized phosphate
> groups. I started by creating copies of original, non-terminal nucleic
> residues and replacing an oxygen of the phosphate (O1P or O2P) with a methyl
> group in xLEaP. I saved this new residue as pdb and mol2 files and I then
> tried to use antechamber to calculate the charge distribution and I get the
> following error:
> Error: cannot run "$AMBERHOME/bin/sqm -O -i -o sqm.out" of bcc() in
> charge.c properly, exit
> I replaced the path with $AMBERHOME for clarity. I have tried to modify the
> PDB file to have the same structure as the sustiva.pdb from the tutorial and
> yet I still get the same error. Other charge methods produce similar or
> other types of error. Alternatively, I tried to use R.E.D. but it seems that
> I need Gaussian or GAMESS to complete the procedure and I do not have
> those.
> Any idea what could be wrong? Is there an alternative method of doing this?
> Any help would be much appreciated.
> Thank you,
> Sasha.

AMBER mailing list
Received on Thu Jun 16 2011 - 23:00:03 PDT
Custom Search