Hi, Prof. Ren,
I cannot compile tinker4.3 in my x64 machine. It failed with error message
undefined reference to `chksocket_'
Including server.f in the source folder did not solve the problem.
So I followed the second way. All the steps seemed fine.
Tinker_to_amber gave the following output:
frcfieldfile = /home/ymei/tinker6/params/amoebabio09.prm
found a-axis = 68.5238760000000
found b-axis = 71.8084030000000
found c-axis = 68.2765680000000
found alpha = 90.0000000000000
found beta = 90.0000000000000
found gamma = 90.0000000000000
num_xyz_atoms = 26140
numres = 8048
num_atoms = 26140
vdw: num_vdw_types = 19
num_bonds = 18273
num_urey_bradley = 7893
num_tot_angles = 12421
num regular, trigonal angles = 10999 1422
num_out_of_plane_bends = 1422
numtor = 6619
num1,num_torsions = 5747 8964
no success finding Stretch-Torsions
num_pitorsions = 268
num_stretch_bends = 3955
num_tor_tors = 147
num tortor tables = 8
num_molecules = 7896
num_multipoles = 26140
number of frame def list = 60199
num_12 = 18273
num_13 = 12421
num_14 = 6529
num_15 = 7403
I used a cuboid box this time and I recompiled the code with maxatm in sizes.i changed to 50000.
But the generated prmtop file was strange.
I paste some of the lines here
%FLAG POINTERS
%FORMAT(10I8)
26140 1 1 1 1 1 1 1 0 0
44616 8048 1 1 1 1 1 1 1 1
0 0 0 0 0 0 0 1 0 0
0 0
and all the atomic charges were zero.
Best regards,
Ye
2013-03-07
From： Amber Amoeba
Date： 2013-03-07 14:54:50
To： AMBER Mailing List
CC：
Subject： Re: [AMBER] bug report: tinker_to_amber failed forsystemscontainingcounter ions
Ye,
You have a couple of options.
1. You can use the older tinker v4.3 (found here
http://dasher.wustl.edu/tinker/). If you want to use amoebabio09.prm with
this version, you need to back-convert it using amoeba_conv.pl (download
from
http://water.bme.utexas.edu/wiki/index.php/Software:amber). I would
recommend using the "older" version amoebapro04.prm (
http://water.bme.utexas.edu/wiki/index.php/Software:amoeba_bio).
2.If you want to use the latest tinker like you did, please replace
analyze.f with this one: http://biomol.bme.utexas.edu/~pren/tinker_to_amber/.
This fix the ion issue and connectivities that were missing. You still have
to change the "None" in the analout to "Z-then-X" manually for ions. Please
do not change the tinker_to_amber source code. Ignore the warning about the
torsion-torsion spline. It is due to small mismatches at the boundary (e.g.
values 180 and -180 should be exactly the same but actually differ a tiny
bit).
3. No matter you choose 1 or 2, if you are using an octahedron box, you
need to make some manual changes to the inpcrd and prmtop files produced by
the tinker_to_amber. The format is explained in amber manual. The specific
changes are explained here
http://water.bme.utexas.edu/wiki/index.php/Software:amber
Please let me know if you have problems. These changes will be incorporated
into future tinker/amber.
Thanks
Pengyu
On Wed, Mar 6, 2013 at 8:23 PM, Ye MEI <ymei.itcs.ecnu.edu.cn> wrote:
> 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
> >
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Received on Thu Mar 07 2013 - 03:00:03 PST
