Hi Jason,
Thanks for your help. The modified Test.pdb worked well and the number of atoms in the xyz file now is the same
as that in the pdb file. However, Step 3 still did not work, the prmtop and inpcrd files were still empty.
Also I tried to execute the Step 3 interactively and at the end an error message appeared saying there was some trouble on opening the key_file.
-------------------------------------------------------------
[username.host]$ tinker_to_amber
analoutfile:
Test.analout
xyz_file:
Test.xyz
pdb_file:
Test.pdb
title:
Amoeba Fore Field
prmtopfile (output):
Test.prmtop
inpcrd_file (output):
Test.inpcrd
trouble opening key_file
--------------------------------------------
But the content of the key_file is "parameters /home/username/apps/tinker/params/amoebapro13" ( /home/username/apps/tinker is $TINKER_HOME) and also in step 1 the key_file could be open without any problem.
So could give me any help about what happened ?
Thanks again !
Bin
At 2015-10-15 09:09:23,"Jason Swails" <jason.swails.gmail.com> wrote:
>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 Thu Oct 15 2015 - 07:30:07 PDT
