Hi, Prof. Ren,
All the relevant files can be found here:
http://itcs.ecnu.edu.cn/ymei/tinker2amber.zip
The protein myoglobin was solvated in a truncated octahedron water box with two
chloride ions. The whole system was generated by LEaP module in AmberTools 12.
Then I split this pdb file into two files. One only contained the protein. The other file
contained all the atoms. Keeping protein atoms in the second file is to maintain the
correct sequence number for atoms and their connectivities.
I used pdbxyz command to convert two pdb files to xyz files with amoebabio09.prm.
PDB file for the protein was OK. But ions and water molecules need some modifications.
I used the program fix_wat_xyz_amoeba_type.f released with AMBER 12 to change the
atom types to 402 and 403 for oxygen and hydrogen atoms in water molecules, and 412 for
the chloride ions.
Then I removed protein atoms in the second xyz file, and combined two xyz files together.
I also changed the number of atoms in the first line of the combined xyz file.
The ouput of "analyze.x peptide_wat PC >peptide_wat_analout" also seemed fine.
Then I typed 'tinker_to_amber -name peptide_wat -title "amoeba myoblogin" '. It gave warning message:
ISPLPE -- Warning, Input Values to Spline are Not Periodic
and error message
wrong number of fields in multipole line: numf = 4
I have not figured out how to deal with the warning message. I will check the manuals.
The error message was caused by the chloride ions. In line 2459-2476 of tinker_to_amber.f90,
it only handles lines with 6 or 7 fields, and gives error message for other lines. So I changed this
part and you can find the code in the zipped file. This time it finished with only warning messages:
ISPLPE -- Warning, Input Values to Spline are Not Periodic
no success finding Number of 1-2 Pairs!
no success finding Number of 1-3 Pairs!
no success finding Number of 1-4 Pairs!
no success finding Number of 1-5 Pairs!
I guess there may be something wrong with the key file.
The prmtop file was not correctly generated.
So now I am wondering
1. Is the new tinker_to_amber.f90 code correct?
2. Should I add more control options into the key file?
I am using tinker-6.1.01 compiled with intel compiler in an x64 machine.
I can run md simulations with command dynamic.x.
All the best,
Ye
2013-03-06
From£º Amber Amoeba
Date£º 2013-03-06 04:34:19
To£º ymei; amber
CC£º
Subject£º [AMBER] bug report: tinker_to_amber failed for systems containingcounter ions
Hi Ye,
Can you tell me which version of tinker (analyze) are you using?
How did you add the metal ions into tinker xyz and PDB files?
After you prepare the tinker files, before you run tinker_to_amber, were
you able to run tinker analyze or minimize and get an energy?
Thanks
Pengyu Ren
UT Austin
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Received on Wed Mar 06 2013 - 00:30:02 PST
