AMBER Archive (2006)

Subject: AMBER: How to calculate the mmpbsa for explicit MD ?

From: jitrayut jitonnom (
Date: Mon Jun 12 2006 - 11:41:52 CDT

Dear amber users

I am new for mmpbsa and I look at the mmpbsa tutorial which is an implicit
md. For explicit MD, I found the error say that "NATOM mismatch between
topology and coordinate" in sander output. I think that maybe somethings
wrong in step of generating topology of COM,LIG and REC. So, I want any
suggestions about generating topology file for explicit MD.

Thanks in advance for any suggestions

Best regards


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