Dear Amber Users,
I have found a solution to the problem detailed below. Using the Windows version of g09, the molecule.esp file was not written or I didn't find it. Thus repeated the whole process in Linux and noted the presence of the molecule.esp file. Giving the following antechamber command now allowed the computation to finish.
antechamber -i MOS.esp -fi gesp -o MOS.prepin -fo prepi -c resp -rn MOS -s 2
-at amber
We will now see if we can prepare inpcrd and prmtop files for an MD simulation. Our interest is the modeling of the flexible loops on the exterior of this large protein, and not the details of the metal center geometry. The file 1fo4 has many missing residues, which we have added with the program modeller. We are using hydrodynamic computations to test the accuracy of the final structures obtained.
Cheers, Sergio
-----Original Message-----
From: Sergio R Aragon [mailto:aragons.sfsu.edu]
Sent: Monday, April 29, 2013 5:58 PM
To: amber.ambermd.org
Cc: Eric Anderson
Subject: [AMBER] antechamber espgen error for molybdenum complex:fitting values are missing
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 - 20:00:02 PDT
