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
those.
Any idea what could be wrong? Is there an alternative method of doing this?
Any help would be much appreciated.
Thank you,
Sasha.
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Received on Thu Jun 16 2011 - 14:00:04 PDT
