Hi All,
I tried to generate the prmtop and inpcrd files of a protein by using the Amoeba Force Field. I did exactly according to the Amber 14 manual.
First, I installed Tinker( tinker-6.3.3.tar.gz , the amber 14 has already been installed). Then I typed the following commands:
step 1: echo ˇ°parameters $TINKER_HOME/params/amoebapro13ˇ± > Test.key
step 2: analyze Test PC > Test.analout
step 3: tinker_to_amber -name Test -title ˇ°Test Amoeba FFˇ±
(The attachment is the Test.pdb file)
The first 2 steps worked well and I can see the corresponding output files, but the Step 3 failed, It just gave out empty prmtop and inpcrd files.
Also I compared the Test.xyz file with the Test.pdb file and I found that the number of atoms was not the same. In the xyz file, it omitted the OXT atom( terminal oxygen) of the first chain, but kept the OXT atom of another chain ( there are 2 chains in Test.pdb ). Also the xyz file omitted some hydrogen atoms of the starting GLY in the second chain.
So could anyone give some suggestions and help ?
Thanks in advance !
Bin
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- application/octet-stream attachment: Test.pdb
Received on Wed Oct 14 2015 - 15:00:03 PDT
