On Wed, Oct 14, 2015 at 5:52 PM, Sun <sunbintyy.163.com> wrote:
> 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 “parameters $TINKER_HOME/params/amoebapro13” > Test.key
> step 2: analyze Test PC > Test.analout
> step 3: tinker_to_amber -name Test -title “Test Amoeba FF”
> (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 ?
>
The main problem here is that Tinker uses the chain ID to identify where
one chain terminates and the next begins while Amber uses TER cards. So
Tinker, thinking that SER 93 and GLY 94 are part of the same chain,
helpfully eliminates the OXT atom and links them together with a covalent
bond.
What you need to do is to add a chain ID (in the correct column), marking
residues 1 to 93 as chain A and residues 94 to 186 as chain B. I attach a
modified version of Test.pdb where I have done this to show you an example.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 14 2015 - 18:30:03 PDT
