Dear amber user,
I tried to use ff12SB force field to run amber tutorial A3 in amber10. I
created the prmtop and inpcrd files with tleap in ambertools12.
Then I run the MD with Amber10. The input files(min.in, heat.in, density.in
, equil.in, and prod.in ) were downloaded form Tutorial website directly.
Everything is fine, however, when I used mm_pbsa.pl from Amber 10 to do
decomposition.
（command line: $AMBERHOME/bin/mm_pbsa.pl decomp.in > decomp.log 2>&1）
I see an error as the following.
bad atom type: 2C
/home/linda/amber10/exe/sander -O -i sander_com.in -o
sander_com.1.out -c ./snapshot/snapshot_com.crd.1 -p ./ras-raf.prmtop not
successful
The output files, topology files, and extracted snapshots from MD
trajectory are pasted in attachment.
Moreover, it runs properly when I perform free energy decomposition using the
topology files and the mdcrd file downloaded from tutorial website.
It would work properly too when I used ff03.r1 force field.
Is ff12SB force field not used in amber10 for decomposing free energy?
I found the sentence"Note:ff12SB calculations must be carried out with
Amber12 if using GB7, GB8, or GBSA" from AmberTools12 Manual.
Any insight would be appreciated.
Hang
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Received on Sun Sep 09 2012 - 01:30:04 PDT
