I ran MD on a protein with bound Mg-ATP. I managed to get the full system built by including the Mg as a separate ion in its own residue, not as part of the ligand. So that went well in that the Mg maintained its position with regard to the ATP in the simulation. But now I want to compute the binding free energy between MgATP and protein. Does anyone have any recommendations as to how to get the 'ligand' prmtop? for ATP, I used the files from
http://www.pharmacy.manchester.ac.uk/bryce/amber#org. When I tried using Antechamber for MgATP, I got the error below, which is why I went with ATP as a residue & Mg as an ion originally:
For atom[44]:MG, the best APS is not zero, bonds involved by this atom are frozen
---Judge bond type for Residue 1 with ID of 1 and Name of MTP ---
---Judge bond type for Residue 2 with ID of 2 and Name of MTP ---
Total number of electrons: 256; net charge: 0
Running: /usr/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/usr/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
Thanks!
Irene Newhouse
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Received on Wed Jul 27 2011 - 15:00:03 PDT
