I just put the pdb file into the zipped folder. Please download it again.
http://itcs.ecnu.edu.cn/ymei/tinker2amber.zip
I forgot to mention that I had moved the atomic name of Cl- one column to the right before running pdbxyz.
Otherwise the code cannot recognize it.
Ye
2013-03-07
From： Amber Amoeba
Date： 2013-03-07 02:29:16
To： AMBER Mailing List
CC：
Subject： Re: [AMBER] bug report: tinker_to_amber failed for systemscontainingcounter ions
Ye,
Can you also provide the matching pdb file? There is some format changes in
the recent tinker. I will get it fixed.
On Wed, Mar 6, 2013 at 2:19 AM, Ye MEI <ymei.itcs.ecnu.edu.cn> wrote:
> 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： Amber Amoeba
> Date： 2013-03-06 04:34:19
> To： ymei; amber
> CC：
> Subject： [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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 06 2013 - 18:30:02 PST
