Dear AMBER users,
I have two problems while using mm_pbsa, so I send this mail for help.
First is the error "bad atom type: F" of decomposition using mm_pbsa, I have open the file mdread.f, but I don't know how to add the parameters of atom F, and what is its parameters?
Second is the problem of alanine scanning, I have thought that I had done it, but I was wrong. It shows in the terminal window as "/home/yfqi/bin/amber9/exe/sander -O -i sander_com.in -o sander_com.1.out -c ./1xkk_com.crd.1 -p ../com.prmtop not successful". And I find this in the output file: FATAL: NATOM mismatch in coord and topology files. But I am confused, I have calculated the free energy using the same files and parameters as used in the alanine scanning, why calculation of free energy succeeded, while alanine scanning failed.
The attachment are input and output file used in the calculation of alanine scanning. Any responses will be appreciated!
All the best,
Qinghua Liao
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Received on Sat May 23 2009 - 01:09:51 PDT
