AMBER Archive (2009)

Subject: 回复： [AMBER] number_rec_numbers in mm_pbsa

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Mon Apr 06 2009 - 19:18:54 CDT

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_at_elan.com>
收件人： AMBER Mailing List <amber_at_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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