[AMBER] bug report: tinker_to_amber failed for systems containing counter ions

From: Ye MEI <ymei.itcs.ecnu.edu.cn>
Date: Tue, 5 Mar 2013 12:54:51 +0800

Dear Amber developer,

I am trying to employ Amoeba force field (amoebabio09.prm from Tinker 6.1.01) into AMBER12 to simulate a charged protein in periodic water box.
Two chloride ions were added to neutralize the system.
I followed the instruction in the folder $AMBERHOME/src/pmemd.amoeba/build_amoeba/examples/JAC to generate the files.
Everything was fine before I typed tinker_to_amber. The program failed with error message:

wrong number of fields in multipole line: numf = 4

After I read the code and looked through the analout file, I found that the program failed when it was dealing with the chloride ions.
In section "Atomic Multipole Parameters", the lines for the chloride ions read

  2460 2460 None -1.00000
                                                    0.00000 0.00000 0.00000
                                                    0.00000 0.00000
                                                    0.00000 0.00000 0.00000
  2461 2461 None -1.00000
                                                    0.00000 0.00000 0.00000
                                                    0.00000 0.00000
                                                    0.00000 0.00000 0.00000

Because chloride ions do not have any connectivities, the third and the fourth fields are missing. The tinker_to_amber code cannot deal with these lines.
Can anyone help update this code?

Best regards,

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Received on Mon Mar 04 2013 - 21:00:03 PST
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