Hi Mr Zhu,
I want to ask you a question, why you set your NUMBER_REC_GROUPS as 2? I can't understand that. I also use mm-pbsa to calculate binding energy between ligands and receptors, but I set that parameter as 1.Could you explain it for me? Thanks very much!
All the best,
Qinghua Liao
________________________________
发件人： "Zhu, Yong-Liang" <Yong-Liang.Zhu.elan.com>
收件人： AMBER Mailing List <amber.ambermd.org>
已发送： 2009/4/7(周二), 上午7:52:06
主题： [AMBER] number_rec_numbers in mm_pbsa
Hello there,
I use Amber 10. The complex has protein residues from atom 1-5600, then
ligand 5601-5700, then water 5701-10000.
So in mm_pbsa input file, I have this:
NUMBER_LIG_GROUPS 1
LSTART 5601
LSTOP 5700
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 5600
RSTART 8000
RSTOP 8002
However, mm_pbsa failed as it complained "NATOM mismatch in coord and
topology file.
Ambpdb could not convert the extracted complex rst to pdb file either.
What is wrong? Do I need extra topology file for just the water
molecule?
Thanks,
Young
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Received on Wed Apr 08 2009 - 01:13:37 PDT
