From: John Wise (jwise_at_mail.smu.edu)
Date: Tue Jul 25 2006 - 14:46:35 CDT
Peter,
That was it. Now it's ATP! I will have to be more careful with the
differences between pdb and the topology names in the future. Thank you
very much.
Regards,
John
Peter Freddolino wrote:
> Dear John,
> in both cases, the problem appears to be that the nomenclature between
> the heavy atoms of your pdb file and the topology file. After I
> renamed these atoms (replacing all instances of * with ') I got an atp
> molecule with the correct chirality. I have attached my modified input
> and output pdb; please verify that you can reproduce this. This
> problem is also what is causing the coordinates to look pretty bad in
> your output files -- you're getting guessed coordinates for the entire
> sugar.
> Best,
> Peter
>
>
> John Wise wrote:
>
>> Peter,
>> Sorry for the mangled files. Please find attached a tarball with all
>> relevant files. I appreciated your taking a look.
>> Regards,
>> John
>>
>> Peter Freddolino wrote:
>>
>>> Hi John,
>>> could you please compress and resend the attached files to avoid
>>> having them get mangled by email? This sounds very surprising
>>> because psfgen should not touch the coordinates of heavy atoms that
>>> are already present. In any case, I'll have a look.
>>> Thanks,
>>> Peter
>>>
>>> John Wise wrote:
>>>
>>>> Dear Listmembers,
>>>>
>>>> If you use ATP residues built by psfgen and CHARMM27 All-Hydrogen
>>>> Nucleic Acid Topology Files, I believe that the resulting molecule
>>>> has mistakes in its chiral centers that may introduce artifacts in
>>>> your simulation results.
>>>>
>>>> Our group does ESR measurements using various stable radical
>>>> molecular probes and one of these is a modified ATP molecule. In
>>>> the process of building and testing topology and parameter files
>>>> for simulating this new residue, I have noticed that psfgen inverts
>>>> the configuration of the C1' and C3' chiral centers when it builds
>>>> an all hydrogen ATP using crystallographic (heavy atom) coordinates
>>>> of ATP. This will definitely spoil any analysis using this ATP
>>>> residue since the molecule built by psfgen is not ATP (it does not
>>>> contain ribose, but an enantiomer of ribose).
>>>>
>>>> For example, using the top_all27_prot_na.inp topology file and ATP
>>>> coordinates taken from 1DX4 (see atp.pdb below), building an all
>>>> hydrogen ATP results in inverted chiral centers at C1' and C3' (or
>>>> relatively speaking C2' and C4'). The incorrect configuration is
>>>> visible right away, even though the top_all27_prot_na_inp topology
>>>> file fails to set the C4' hydrogen. It is easier to see after
>>>> minimization (see the resulting minimized "incorrect ATP" -
>>>> atp_test_min.pdb below). The problem is that the configuration at
>>>> these chiral atoms is correct in the original heavy atom pdb
>>>> coordinates, but I believe psfgen sets them wrong while it is
>>>> building the all hydrogen ATP.
>>>>
>>>> Viewing the correct configuration for beta-D-ribofuranosyl residues
>>>> in ATP in either C3'-endo or C2'-endo forms has the adenine and C5'
>>>> substituents on the opposite "side" of the ring to the C2'- and
>>>> C3'-OH groups. psfgen does not get this correct.
>>>>
>>>> I have included the build script (atp_test.pgn) and the
>>>> minimization script (atp_test_min.conf) for anyone interested in
>>>> reproducing this (see below). Note that if you try to reproduce
>>>> this with the minimization using par_all27_prot_na_lipids_full.inp
>>>> with ATP built with top_all27_prot_na.inp you will have to change
>>>> the C2' and C4' ATOM-types for residue ATP in top_all27_prot_na.inp
>>>> to CN7B and CN8B respectively (see old posts in the list for
>>>> resolution of this problem).
>>>>
>>>> Variations I have tried include:
>>>> (a) Eliminating the chiral atoms from the coordinate file and
>>>> relying on the IC table to set them. Still does not result in the
>>>> correct chiral configurations.
>>>>
>>>> (b) I have tried a number of coordinates for ATP from other pdb
>>>> files - same result.
>>>>
>>>> (c) Using the latest top and par files (c32b1) - same result.
>>>>
>>>> (d) Rewriting the IC table using an experimentally (NMR) determined
>>>> all hydrogen ATP analog structure to explicitely set the chirality
>>>> at all of the chiral centers in the IC table. (Anyone who wants
>>>> these new top files, please ask and I'll send them right out.)
>>>> Although the new topology file results in correct configurations at
>>>> C1', C2' and C4' (and the C4' hydrogen sets properly), the
>>>> resultant "ATP" still does not have the correct configuration for
>>>> the C3' atom.
>>>>
>>>> I am really perplexed by this and am running out of ideas to try.
>>>>
>>>> It would be great if someone could prove me wrong about this!
>>>> Any help would be greatly appreciated.
>>>>
>>>> Thanks in advance,
>>>> John
>>>>
>>>> Files to reproduce this:
>>>>
>>>> (If you use top_all27_prot_na.inp, don't forget to change the C2'
>>>> and C4' ATOM types - see above).
>>>>
>>>>
>>>> atp.pdb (original no hydrogen coordinates from 1DX4)
>>>>
>>>> CRYST1 177.820 68.989 56.593 90.00 104.15 90.00 P 1 1
>>>> ATOM 1 PG ATP X 676 14.097 0.957 15.066 1.00
>>>> 15.67 ATOM 2 O1G ATP X 676 15.430 0.883
>>>> 15.756 1.00 17.70 ATOM 3 O2G ATP X 676 12.862
>>>> 0.767 15.836 1.00 15.53 ATOM 4 O3G ATP X 676
>>>> 14.243 -0.076 13.974 1.00 13.95 ATOM 5 PB ATP X
>>>> 676 14.852 3.282 13.423 1.00 12.74 ATOM 6
>>>> O1B ATP X 676 16.289 2.919 13.320 1.00 15.00
>>>> ATOM 7 O2B ATP X 676 14.475 3.413 12.017 1.00
>>>> 15.72 ATOM 8 O3B ATP X 676 13.934 2.348
>>>> 14.286 1.00 15.28 ATOM 9 PA ATP X 676 15.477
>>>> 5.919 14.499 1.00 13.47 ATOM 10 O1A ATP X 676
>>>> 16.312 5.772 15.724 1.00 13.31 ATOM 11 O2A ATP X
>>>> 676 16.224 6.277 13.300 1.00 13.42 ATOM 12
>>>> O3A ATP X 676 14.624 4.611 14.270 1.00 11.30
>>>> ATOM 13 O5* ATP X 676 14.361 6.949 14.812 1.00
>>>> 15.95 ATOM 14 C5* ATP X 676 13.331 7.464
>>>> 13.937 1.00 13.15 ATOM 15 C4* ATP X 676 12.244
>>>> 8.018 14.821 1.00 13.39 ATOM 16 O4* ATP X 676
>>>> 12.824 9.043 15.673 1.00 15.92 ATOM 17 C3* ATP X
>>>> 676 11.052 8.645 14.062 1.00 15.86 ATOM 18
>>>> O3* ATP X 676 9.792 8.347 14.700 1.00 16.75
>>>> ATOM 19 C2* ATP X 676 11.403 10.126 14.183 1.00
>>>> 16.79 ATOM 20 O2* ATP X 676 10.264 10.991
>>>> 14.099 1.00 16.14 ATOM 21 C1* ATP X 676 12.108
>>>> 10.232 15.567 1.00 14.13 ATOM 22 N9 ATP X 676
>>>> 12.937 11.424 15.757 1.00 12.81 ATOM 23 C8 ATP X
>>>> 676 13.995 11.865 15.027 1.00 10.25 ATOM 24
>>>> N7 ATP X 676 14.490 13.007 15.514 1.00 15.38
>>>> ATOM 25 C5 ATP X 676 13.697 13.308 16.608 1.00
>>>> 13.47 ATOM 26 C6 ATP X 676 13.689 14.373
>>>> 17.556 1.00 15.40 ATOM 27 N6 ATP X 676 14.530
>>>> 15.409 17.536 1.00 19.72 ATOM 28 N1 ATP X 676
>>>> 12.752 14.389 18.568 1.00 14.41 ATOM 29 C2 ATP X
>>>> 676 11.837 13.329 18.635 1.00 11.77 ATOM 30
>>>> N3 ATP X 676 11.766 12.299 17.803 1.00 9.60
>>>> ATOM 31 C4 ATP X 676 12.738 12.329 16.802 1.00
>>>> 9.57 END
>>>>
>>>>
>>>> atp_test.pgn (the script I used to build atp_test.psf and
>>>> atp_test.pdb)
>>>>
>>>> # You need to create working directory "output" in the build
>>>> directory;
>>>> # You need to remove old output files before running again
>>>> # from shell, run: rm -f output/*.pdb output/*.psf
>>>> resetpsf
>>>> package require psfgen
>>>> # correct topology file needs to be in ../toppar
>>>> topology ../toppar/top_all27_prot_na.inp
>>>> # atp.pdb needs to be in ../common
>>>> segment X {
>>>> pdb ../common/atp.pdb
>>>> }
>>>> # patches should be added here
>>>> writepsf output/atp_test.psf
>>>> pdbalias residue HIS HSE
>>>> pdbalias atom ILE CD1 CD
>>>> coordpdb ../common/atp.pdb X
>>>> guesscoord
>>>> writepdb output/atp_test.pdb
>>>> # exit
>>>>
>>>> atp_test_min.conf (the conf file to minimize the ATP in vacuo)
>>>>
>>>> #############################################################
>>>> ## JOB DESCRIPTION ##
>>>> #############################################################
>>>> # Minimization of
>>>> # atp_test
>>>> # in vacuo
>>>> #
>>>> #############################################################
>>>> ## ADJUSTABLE PARAMETERS ##
>>>> #############################################################
>>>> structure ../common/atp_test.psf
>>>> coordinates ../common/atp_test.pdb
>>>> set outputname atp_test_min
>>>> set temperature 310
>>>> firsttimestep 0
>>>> #############################################################
>>>> ## SIMULATION PARAMETERS ##
>>>> #############################################################
>>>> # Input
>>>> paraTypeCharmm on
>>>> parameters ../toppar/par_all27_prot_na_lipids_full.inp
>>>> temperature $temperature ;# if restarting
>>>> # Force-Field Parameters
>>>> exclude scaled1-4
>>>> 1-4scaling 1.0
>>>> cutoff 12.
>>>> switching on
>>>> switchdist 10.
>>>> pairlistdist 13.5
>>>> # Integrator Parameters
>>>> timestep 1.0 ;# 1fs/step
>>>> # rigidBonds water ;# "all" needed for 2fs steps
>>>> nonbondedFreq 1
>>>> fullElectFrequency 2 stepspercycle 10
>>>> # Constant Temperature Control
>>>> langevin on ;# do langevin dynamics
>>>> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
>>>> langevinTemp $temperature
>>>> langevinHydrogen off ;# don't couple langevin bath to
>>>> hydrogens
>>>> # Output
>>>> outputName $outputname
>>>> restartfreq 500 ;# 500steps = every 1/2 ps
>>>> dcdfreq 500 ;# 500steps = every 1/2 p
>>>> xstFreq 250
>>>> outputEnergies 100
>>>> outputPressure 100
>>>> outputTiming 1000
>>>> # minimize
>>>> minimize 3000
>>>>
>>>>
>>>>
>>>>
>>>> atp_test_min.pdb (results of the psfgen build and namd2 minimization)
>>>>
>>>> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
>>>> ATOM 1 C4' ATP X 676 13.847 8.387 15.083 1.00
>>>> 0.00 X ATOM 2 H4' ATP X 676 14.762 8.884
>>>> 14.696 1.00 0.00 X ATOM 3 O4' ATP X 676 13.327
>>>> 9.230 16.160 1.00 0.00 X ATOM 4 C1' ATP X 676
>>>> 12.351 10.102 15.638 1.00 0.00 X ATOM 5 H1' ATP X
>>>> 676 11.399 9.843 16.156 1.00 0.00 X ATOM 6
>>>> C5 ATP X 676 12.886 13.573 16.529 1.00 0.00 X
>>>> ATOM 7 N7 ATP X 676 14.104 13.281 15.924 1.00
>>>> 0.00 X ATOM 8 C8 ATP X 676 13.975 12.023
>>>> 15.572 1.00 0.00 X ATOM 9 H8 ATP X 676 14.744
>>>> 11.423 15.076 1.00 0.00 X ATOM 10 N9 ATP X 676
>>>> 12.754 11.478 15.896 1.00 0.00 X ATOM 11 N1 ATP X
>>>> 676 11.142 14.717 17.658 1.00 0.00 X ATOM 12
>>>> C2 ATP X 676 10.441 13.585 17.551 1.00 0.00 X
>>>> ATOM 13 H2 ATP X 676 9.433 13.610 17.975 1.00
>>>> 0.00 X ATOM 14 N3 ATP X 676 10.798 12.416
>>>> 17.020 1.00 0.00 X ATOM 15 C4 ATP X 676 12.045
>>>> 12.474 16.518 1.00 0.00 X ATOM 16 C6 ATP X 676
>>>> 12.394 14.740 17.148 1.00 0.00 X ATOM 17 N6 ATP X
>>>> 676 13.115 15.865 17.278 1.00 0.00 X ATOM 18
>>>> H61 ATP X 676 12.704 16.608 17.795 1.00 0.00 X
>>>> ATOM 19 H62 ATP X 676 14.071 15.886 17.001 1.00
>>>> 0.00 X ATOM 20 C2' ATP X 676 12.213 9.833
>>>> 14.151 1.00 0.00 X ATOM 21 H2'' ATP X 676 12.822
>>>> 10.542 13.546 1.00 0.00 X ATOM 22 O2' ATP X 676
>>>> 10.866 9.864 13.728 1.00 0.00 X ATOM 23 H2' ATP X
>>>> 676 10.777 9.099 13.136 1.00 0.00 X ATOM 24
>>>> C3' ATP X 676 12.769 8.438 13.992 1.00 0.00 X
>>>> ATOM 25 H3' ATP X 676 12.028 7.629 14.197 1.00
>>>> 0.00 X ATOM 26 O3' ATP X 676 13.335 8.323
>>>> 12.683 1.00 0.00 X ATOM 27 H3T ATP X 676 13.776
>>>> 7.420 12.629 1.00 0.00 X ATOM 28 C5' ATP X 676
>>>> 14.192 7.004 15.635 1.00 0.00 X ATOM 29 H5' ATP X
>>>> 676 13.305 6.332 15.526 1.00 0.00 X ATOM 30
>>>> H5'' ATP X 676 14.403 7.068 16.723 1.00 0.00 X
>>>> ATOM 31 O5' ATP X 676 15.384 6.497 14.996 1.00
>>>> 0.00 X ATOM 32 PA ATP X 676 15.311 5.411
>>>> 13.826 1.00 0.00 X ATOM 33 O1A ATP X 676 16.703
>>>> 4.909 13.752 1.00 0.00 X ATOM 34 O2A ATP X 676
>>>> 14.848 6.259 12.693 1.00 0.00 X ATOM 35 O3A ATP X
>>>> 676 14.393 4.431 14.523 1.00 0.00 X ATOM 36
>>>> PB ATP X 676 13.445 3.809 13.391 1.00 0.00 X
>>>> ATOM 37 O1B ATP X 676 14.245 3.181 12.234 1.00
>>>> 0.00 X ATOM 38 O2B ATP X 676 12.390 4.879
>>>> 13.047 1.00 0.00 X ATOM 39 O3B ATP X 676 12.735
>>>> 2.599 14.303 1.00 0.00 X ATOM 40 PG ATP X 676
>>>> 11.610 1.380 14.531 1.00 0.00 X ATOM 41 O1G ATP X
>>>> 676 12.362 0.223 15.197 1.00 0.00 X ATOM 42
>>>> O2G ATP X 676 10.532 1.954 15.453 1.00 0.00 X
>>>> ATOM 43 O3G ATP X 676 11.054 0.988 13.162 1.00
>>>> 0.00 X END
>>>>
>>>
>>
-- John G. Wise, Ph.D. Department of Biological Sciences Southern Methodist University Dallas, TX 75275 Office - Room 332 Dedman Life Sciences Tel. 214 768 3426
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