Dear Amber Users,
We are studying 1fo4, a protein that contains several metal centers including an Iron sulfur complex and a molybdenum sulfur complex. We are able to do Gaussian 09 (either go9w, or Linux Version C.01) calculations to optimize model structures for these complexes, and obtain ESP data. We run into problems using antechamber in the effort to generate mol2 files to use eventually in tleap for MD simulation input. We have updated our Amber12 installation with the recently announced AmberTools 13.
Here is our command and antechamber output:
"esm>antechamber -fi gout -fo mol2 -c resp -i MOS_DFT_LANDZ_EPS.LOG -o MOS.in -rn MOS
For atom[1]:Mo1, the best APS is not zero, bonds involved by this atom are frozen
For atom[2]:O1, the best APS is not zero, bonds involved by this atom are frozen
For atom[3]:S1, the best APS is not zero, bonds involved by this atom are frozen
Error: the ESP fitting centers exist, but the fitting values are missing
It is recommened to generate esp file for resp fitting from the gesp file generated by adding keyword 'iop(6/50=1) in G09 input'
Error: cannot run "/home/apps/amber/amber12/bin/espgen -o ANTECHAMBER.ESP -i MOS_DFT_LANDZ_EPS.LOG" in resp() of charge.c properly, exit"
The file ANTECHAMBER.ESP produced during the run is actually empty. We run Gaussian with the following keywords: pop=(mk,readradii) iop(66/33=2,6/42=6,6/50=1) as recommended. The Mo atom is given a radius of 2.00 at the end of the Gaussian input file. Apart from the frozen bonds, the main issue is that the resp charges are not obtained and we cannot proceed.
We'd appreciate any input that helps us surmount this issue. Thanks,
Sergio Aragon
San Francisco State University/Chemistry
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Received on Mon Apr 29 2013 - 18:30:02 PDT
