Generates the modern PDB format for hydrogen atoms; by default the old format is generated. With one exception only hydrogen atoms are affected; in Arginine, and only if necessary, the nitrogen atoms of the guanidine group are re-numbered. The format for the rest of atoms must come either from the original PDB label or be generated by MOPAC. If MOPAC generates the format, much of the fine detail is lost, so for example in phenylalanine the labels for Cδ1 and Cδ2 might be swapped round.
NEWPDB was added because some programs, e.g., Molprobity, either will not accept hydrogen atoms labeled with the old format or will require existing hydrogen atoms to be removed and new ones added using the new format. In this latter case all information about the original hydrogen atoms, including their existence, is lost. The rules used by NEWPDB are taken from http://publications.iupac.org/pac/pdf/1998/pdf/7001x0117.pdf, Fig. 1 on page 122, "For example, if tetrahedral carbon C has four substituents X, Y, Z, and Z' (with priority X > Y > Z = Z'; i.e., Z and Z are diastereotopic substituents designated provisionally as unprimed and primed), their numbering is derived as follows: if one sights down the X-C axis (with the X atom toward the viewer), the equivalent atoms, Z and Z', are designated Z2 and Z3, such that Y, Z2,and Z3 follow a clockwise orientation." and related directives.
Molprobity is widely used in validating proteins, particularly those reported in the Protein Data Bank. There are two important quantities used in determining the quality of a calculated protein structure. One is the Root-Mean-Square error between the calculated and observed (X-ray or NMR) structures. Calculation of this quantity is straightforward and can be done in MOPAC using COMPARE. The other is a measure of the close contacts between pairs of atom that would be expected to have little or no interaction. Within Molprobity these contacts are called "clashes." Its reports of clashes are accurate, detailed, and of course very useful. However, because Molprobity is optimized for analyzing experimental rather than theoretically predicted structures, when calculated geometries are examined, an unexpected complication arises.
By default, Molprobity will add hydrogen atoms to a PDB geometry. This is, of course, very useful when experimental geometries, which often don't include hydrogen atoms, are being studied. If a PDB geometry does include hydrogen atoms, these are deleted, and the hydrogenation performed by Molprobity is used. At this point, two issues arise when calculated geometries are used: Molprobity does not add hydrogen atoms to water molecules, and it also does not protonate carboxylate groups. Modeling protein geometries requires as realistic a model as possible, so in addition to needing proteins to be hydrogenated all water molecules must also be hydrogenated, and those carboxylate groups that should be neutral must also have a proton on one or other of the oxygen atoms. If these hydrogen atoms are deleted, any complications that might be caused by their presence would go unreported.
Although the option exists in Molprobity to use the hydrogenation from the PDB file this option only works well if the hydrogen atoms are in the modern PDB format. This requirement was the motivation for making the keyword NEWPDB . If the old PDB format is used Molprobity might report severe errors that are, in fact, non-existent.
The eleventh datum on each line in the old format is used in the HTML file generated by keyword HTML to indicate the atomic partial charge. Because this datum is not used by MOPAC, it is not read in, and therefore if NEWPDB is present this datum is set to zero by default. That is, NEWPDB is treated in the same way as SITE or ADD-H, or any other keyword that modifies the data-set. Of course, if a subsequent calculation, e. g., 1SCF, that generates partial atomic charges is present then the eleventh datum will reflect that.
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Old format |
Modern format |
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ATOM 1 N ARG A 1 -0.939 4.862 -12.505 1.0 -6.04 PROT N ATOM 2 CA ARG A 1 -2.167 5.062 -11.709 1.0 -1.52 PROT C ATOM 3 C ARG A 1 -3.087 6.117 -12.344 1.0 2.90 PROT C ATOM 4 O ARG A 1 -4.303 6.068 -12.241 1.0 -7.51 PROT O ATOM 5 CB ARG A 1 -1.773 5.462 -10.276 1.0 -2.95 PROT C ATOM 6 CG ARG A 1 -2.933 6.093 -9.489 1.0 -2.92 PROT C ATOM 7 CD ARG A 1 -4.077 5.096 -9.225 1.0 -0.82 PROT C ATOM 8 NE ARG A 1 -3.590 4.032 -8.311 1.0 -4.78 PROT N ATOM 9 CZ ARG A 1 -4.014 2.740 -8.454 1.0 5.79 PROT C ATOM 10 NH1 ARG A 1 -5.155 2.420 -9.143 1.0 -5.54 PROT N ATOM 11 NH2 ARG A 1 -3.275 1.759 -7.861 1.0 -6.14 PROT N ATOM 12 H ARG A 1 -0.057 5.086 -12.078 1.0 2.16 PROT H ATOM 13 HA ARG A 1 -2.740 4.099 -11.722 1.0 1.24 PROT H ATOM 14 1HB ARG A 1 -1.399 4.559 -9.748 1.0 0.90 PROT H ATOM 15 2HB ARG A 1 -0.914 6.164 -10.292 1.0 1.54 PROT H ATOM 16 1HG ARG A 1 -2.556 6.493 -8.524 1.0 1.27 PROT H ATOM 17 2HG ARG A 1 -3.338 6.979 -10.016 1.0 2.06 PROT H ATOM 18 1HD ARG A 1 -4.919 5.593 -8.696 1.0 1.52 PROT H ATOM 19 2HD ARG A 1 -4.456 4.680 -10.177 1.0 1.98 PROT H ATOM 20 HE ARG A 1 -2.658 4.194 -7.857 1.0 3.40 PROT H ATOM 21 1HH1 ARG A 1 -5.848 3.138 -9.310 1.0 3.45 PROT H ATOM 22 2HH1 ARG A 1 -5.485 1.476 -9.138 1.0 3.23 PROT H ATOM 23 1HH2 ARG A 1 -2.300 1.938 -7.583 1.0 3.48 PROT H ATOM 24 2HH2 ARG A 1 -3.670 0.865 -7.695 1.0 3.28 PROT H |
ATOM 1 N ARG A 1 -0.939 4.862 -12.505 1.0 0.00 PROT N ATOM 2 CA ARG A 1 -2.167 5.062 -11.709 1.0 0.00 PROT C ATOM 3 C ARG A 1 -3.087 6.117 -12.344 1.0 0.00 PROT C ATOM 4 O ARG A 1 -4.303 6.068 -12.241 1.0 0.00 PROT O ATOM 5 CB ARG A 1 -1.773 5.462 -10.276 1.0 0.00 PROT C ATOM 6 CG ARG A 1 -2.933 6.093 -9.489 1.0 0.00 PROT C ATOM 7 CD ARG A 1 -4.077 5.096 -9.225 1.0 0.00 PROT C ATOM 8 NE ARG A 1 -3.590 4.032 -8.311 1.0 0.00 PROT N ATOM 9 CZ ARG A 1 -4.014 2.740 -8.454 1.0 0.00 PROT C ATOM 10 NH1 ARG A 1 -5.155 2.420 -9.143 1.0 0.00 PROT N ATOM 11 NH2 ARG A 1 -3.275 1.759 -7.861 1.0 0.00 PROT N ATOM 12 H ARG A 1 -0.057 5.086 -12.078 1.0 0.00 PROT H ATOM 13 HA ARG A 1 -2.740 4.099 -11.722 1.0 0.00 PROT H ATOM 14 HB2 ARG A 1 -1.399 4.559 -9.748 1.0 0.00 PROT H ATOM 15 HB3 ARG A 1 -0.914 6.164 -10.292 1.0 0.00 PROT H ATOM 16 HG2 ARG A 1 -2.556 6.493 -8.524 1.0 0.00 PROT H ATOM 17 HG3 ARG A 1 -3.338 6.979 -10.016 1.0 0.00 PROT H ATOM 18 HD2 ARG A 1 -4.919 5.593 -8.696 1.0 0.00 PROT H ATOM 19 HD3 ARG A 1 -4.456 4.680 -10.177 1.0 0.00 PROT H ATOM 20 HE ARG A 1 -2.658 4.194 -7.857 1.0 0.00 PROT H ATOM 21 HH11 ARG A 1 -5.848 3.138 -9.310 1.0 0.00 PROT H ATOM 22 HH12 ARG A 1 -5.485 1.476 -9.138 1.0 0.00 PROT H ATOM 23 HH21 ARG A 1 -2.300 1.938 -7.583 1.0 0.00 PROT H ATOM 24 HH22 ARG A 1 -3.670 0.865 -7.695 1.0 0.00 PROT H |