We found a problem converting tinker to amber using the latest tinker v6.
Please use tinker v4.3 and that should work. You can convert tinker
parameter (prm) file from v6 back to v4.3 using a script amoeba_conv.pl,
which can be downloaded here:
http://water.bme.utexas.edu/wiki/index.php/Software:amber#Important:_read_me_first
)
On Thu, Mar 14, 2013 at 11:43 AM, Ye MEI <ymei.itcs.ecnu.edu.cn> wrote:
> just tried to optimize a structure which had been fully optimized under
> AMBER03 force field.
> I got the same warning message as before. I am afraid there might be
> something wrong in the topology information in the prmtop file.
>
> out of loop, iter,rms = 11 0.9347E-02
> e_rec_perm,e_dir_perm,e_adj_perm,e_self_perm =
> 1765.2620 -101930.0817 273864.9969 -297570.4186
> e_rec_ind,e_dir_ind,e_adj_ind,e_self_ind =
> -344.1877 -52921.2454 -8769.7489 -1445.9543
> e_dir_vdw,e_adj_vdw,e_rec_vdw =
> 81227.5963 1426.8467 -141.3089
> nonbond vir = -128204.98 2210.4094 692.49750
> nonbond vir = 2210.4094 -125526.85 -240.62712
> nonbond vir = 692.49750 -240.62712 -126558.37
> valence energies: bond,ureyb,angle 0.73925310E+04 0.15674701E+12
> 0.84826972E+04
> valence energies: trangle,opbend,tor 324.3290 23.8886
> 313.1189
> valence energies: pitors,strbend,tortor 18.3333 18.2073
> -13.8418
> valence energies: strtor 0.0000
> valence vir = ************** 129198286.1140 43162819.9491
> valence vir = 129198286.1140 ************** -18326200.9617
> valence vir = 43162819.9491 -18326200.9617 **************
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.5675E+11 5.3003E+05 1.9246E+06 H1 26112
> BOND = 7392.5310 ANGLE = ************* DIHED =
> 317.6104
> VDWAALS = 81086.2874 EEL = -123870.2414 HBOND =
> 0.0000
> 1-4 VDW = 1426.8467 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> EPOLAR = -63481.1362
>
>
> Ye
> 2013-03-15
>
>
>
>
> Ye MEI
> 2013-03-15
>
>
> From： Amber Amoeba
> Date： 2013-03-12 02:18:44
> To： AMBER Mailing List
> CC：
> Subject： Re: [AMBER] bug report:
> tinker_to_amberfailedforsystemscontainingcounter ions
>
> Can you optimize the structure in TINKER before converting to amber? Use
> parallel openmp-thread will help speed up a bit.
> It seems that all terms are reasonable except for the angle. I would double
> check the structure and connectivity. Or start with a protein PDB/structure
> that is already optimized.
> On Fri, Mar 8, 2013 at 9:35 AM, Ye MEI <ymei.itcs.ecnu.edu.cn> wrote:
> > 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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Received on Wed Apr 10 2013 - 14:00:34 PDT
