[AMBER] Nucleic residues with methylphosphonates

From: Alexander Drozdetski <adrozdetski.gmail.com>
Date: Thu, 16 Jun 2011 16:49:33 -0400

Hello everyone,

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 sqm.in -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

Any idea what could be wrong? Is there an alternative method of doing this?
Any help would be much appreciated.

Thank you,
AMBER mailing list
Received on Thu Jun 16 2011 - 14:00:04 PDT
Custom Search