Hi, Prof. Ren,
I still cannot get it work.
I tried minimization with the attached input file. Other relevant files can be downloaded from
http://itcs.ecnu.edu.cn/ymei/AmoebaTest.zip
The output energy is weird with abnormally large bending energy
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.5700E+11 5.3046E+05 1.9333E+06 O 26054
BOND = 1562.3590 ANGLE = ************* DIHED = 395.9413
VDWAALS = 28514.7995 EEL = -72710.5133 HBOND = 0.0000
1-4 VDW = 2171.7723 1-4 EEL = 0.0000 RESTRAINT = 0.0000
EPOLAR = -27008.8684
Dipole convergence: rms = 0.985E-02 iters = 10.00
out of loop, iter,rms = 10 0.9847E-02
e_rec_perm,e_dir_perm,e_adj_perm,e_self_perm =
5026.8137 -55712.3506 275540.1023 -297570.4186
e_rec_ind,e_dir_ind,e_adj_ind,e_self_ind =
-470.1890 -21441.8769 -4358.6416 -741.0962
e_dir_vdw,e_adj_vdw,e_rec_vdw =
28730.6905 2171.7723 -212.2151
nonbond vir = -49611.408 4194.7509 -2144.7599
nonbond vir = 4194.7509 -51124.669 2564.9863
nonbond vir = -2144.7599 2564.9863 -48412.859
valence energies: bond,ureyb,angle 0.15623844E+04 0.15699537E+12 0.20018563E+04
valence energies: trangle,opbend,tor 796.3284 179.4080 401.4212
valence energies: pitors,strbend,tortor 16.7169 -21.4293 -22.1968
valence energies: strtor 0.0000
valence vir = ************** 214915029.1693 83415569.4066
valence vir = 214915029.1693 ************** **************
valence vir = 83415569.4066 ************** **************
out of loop, iter,rms = 10 0.9847E-02
e_rec_perm,e_dir_perm,e_adj_perm,e_self_perm =
5027.1092 -55717.6459 275538.6938 -297570.4186
e_rec_ind,e_dir_ind,e_adj_ind,e_self_ind =
-470.1654 -21444.7449 -4359.2458 -741.1707
e_dir_vdw,e_adj_vdw,e_rec_vdw =
28735.1026 2171.7723 -212.2151
Is it due that the structure was generated by LEaP without any optimization?
Ye
2013-03-08
From： Amber Amoeba
Date： 2013-03-08 00:05:44
To： AMBER Mailing List
CC：
Subject： Re: [AMBER] bug report: tinker_to_amber failedforsystemscontainingcounter ions
The "atomic charge" is not used. Search for the
"AMOEBA_LOCAL_FRAME_MULTIPOLES_LIST". You should see the charges/dipoles
etc there.
I can't tell what's wrong with the lines you posted. Did you try to run
energy minimization (you may turn off polarization first and then back on).
On Thu, Mar 7, 2013 at 4:31 AM, Ye MEI <ymei.itcs.ecnu.edu.cn> wrote:
> 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
> > > _______________________________________________
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> >
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Received on Fri Mar 08 2013 - 08:00:03 PST
