[AMBER] MM-PBSA energy-decomposition

From: yan zhang <yanzhang086.gmail.com>
Date: Thu, 2 Dec 2010 14:15:59 +0800

Hello sir,

I want to calculate the energy contribution of the key residues'GLU166 (with
H) ' computed by GB method ,so i plan to modify the web-online binding
energy.mmpbsa file.
The moiety of the file needed to be changed is the .DECOMP, and the
descriptors include DCTYPE, COMREC, COMLIG, COMPRI, RECPRI, LIGRES, RECRES,
RECMAP, LIGMAP.
After i ran the job, it showed ‘ wrong format for decomp :GLU166. I wanna
to kown the specific form of these descriptors . The information of the
ligand interacting with the protein in the complex file is 'UNK445'.

Besides , i want to add the entropy calculation, so i edited the .NM moiety
, but it showed that ’ ///sander................not running properly'. The
out file said ' The system has entended beyond the extent of the virtual
box', how can i modify the input file to make the system smaller ? I
attached the sanmin_com.1out file .

Thanks,

Sincerely, YanZhang


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Received on Wed Dec 01 2010 - 23:00:03 PST
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