> 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
> those.
>
> Any idea what could be wrong? Is there an alternative method of doing this?
> Any help would be much appreciated.
>
>
> Thank you,
> Sasha.
