<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font size="3"><span style="font-family: times new roman,new york,times,serif;">I have uploaded to the user contributed software at</span><span style="font-family: times new roman,new york,times,serif;"> gromacs.org a<br>further revision of topolbuild that includes support for OPLS-AA as<br>file topolbuild1_3.tgz </span><br style="font-family: times new roman,new york,times,serif;"></font><div style="font-family: times new roman,new york,times,serif;"><font size="3"><br>topolbuild 1.3<br>Reads a syntactically correct Tripos .mol2 file with charges to generate<br>something approximating gromacs *.gro, *.top, and *.itp files from it<br>based on selected force field parameters. This version adds support for<br>oplsaa. Includes tables to support amber, gaff, glycam, oplsaa, and gmx<br>type force
fields. Requires that the *.mol2 file have syntactically correct<br>Tripos atom types and absolutely will not work with other input atom<br>types. Includes capability of pruning dihedral angles to a possibly more<br>reasonable set. Note that the standard for a syntactically correct mol2<br>file is the Tripos Toolkit Utilities Manual.<br><br>Revisions include:<br> 1. Added OPLS-AA support, atom definition files, and force field<br> data tables. Best results for pruning of dihedral angles will<br> probably be with -purge 0<br> 2. Corrected errors in setting some categories of rings<br> 3. Corrected Makefile to be compatible with more variants of make<br> 4. Increased initial estimate of maximum number of rings for ring<br> detection<br> 5. Added lines to log, topology, and include files to give
version<br> and command line of invocation<br> 6. Made internal rearrangements to ease addition of and handling<br> of other force fields<br> 7. Set default prune of excess dihedral angles equivalent to -purge 1<br> 8. Added option to translate molecule coordinates to center of<br> mass when renumbering is not requested<br> 9. Added elements to internal atomic masses / numbers table<br>10. Revised method of correction of Tripos out of plane pyramid<br> height improper force constants to cosine function force constants<br>11. Altered setting of dihedral phases for Tripos force field<br>12. Changed error messages in mol2 file reading to give clearer<br> statement of problems<br>13. Changed error for not ending the bonds section of the mol2 file<br>
with @<TRIPOS> from fatal error to warning because mol2 files<br> supplied by some databases lack correct termination<br>14. Added atom type default entries to the amber atom type definition<br> tables<br>15. Corrected errors in gromacs topology defaults line settings.<br>16. Changed preferences in dihedral angles purge to choose the<br> maximum number of heavy atoms possible for dihedrals retained<br> for topology output.<br>17. Modified renaming.<br>18. Use of distances and angles measured from structure no<br> longer affects dihedral values.<br>19. Added -charge option to permit assignment of atom charges<br> based on atom type charges from force field. Currently only<br> OPLS-AA tables support this option. <br><br>Special
Processing Used for oplsaa Force Fields<br>With the exception of van der Waals parameters and default atom<br>charges, oplsaa is designed such that force field parameters are<br>associated with atom types from a modified and amplified version<br>of the Kollman atom types. However, oplsaa also uses a much richer<br>set of atom types to determine van der Waals parameters and default<br>atom charges. Therefore, generation of an oplsaa topology requires<br>double determination of atom types. A first determination of atom<br>types is performed with the expanded version of the Kollman atom<br>types. This assignment is used to assign force constants, bond lengths,<br>angles, dihedral angles, and improper angles. A second determination<br>of atom types is performed to assign final oplsaa atom types to match<br>the atom types in ffoplsaanb.itp from the gromacs distribution. A<br>major problem of this double conversion is that topolbuild does not<br>always
select the exact same atom type for a residue listed in<br>ffoplsaa.rtp. The following table gives some of the differences<br>discovered:<br><font size="1"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> residue atom rtp value topolbuild usage</span></font><br><font size="1"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HISA ND1 opls_503 opls_557 imidazole N1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HISA HD1 opls_504 opls_562
imidazole H1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HISA HE1 opls_146 opls_563 imidazole H2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HISB HD2 opls_146 opls_565 imidazole H5</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HISB HE1 opls_146
opls_563 imidazole H2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HISB NE2 opls_503 opls_557 imidazole N1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> HISB HE2 opls_504 opls_562 imidazole H1</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP HD1
opls_146 opls_597 indole H2</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP CE3 opls_145 opls_590 indole C4</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP HE3 opls_146 opls_599 indole H4</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP
CZ2 opls_145 opls_593 indole C7</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP HZ2 opls_146 opls_602 indole H7</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP CZ3 opls_145 opls_591 indole C5</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">
TRP HZ3 opls_146 opls_600 indole H5</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP CH2 opls_145 opls_592 indole C6</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> TRP HH2 opls_146 opls_601 indole H6</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"></font>Because of the manner in
which oplsaa constants were developed<br>originally, in all of these cases the same bond, angle, dihedral, and<br>improper constants are assigned. The van der Waals parameters are identical between the original rtp atom type and the topolbuild choice<br>as well. When charges from the mol2 file rather than the oplsaa atom<br>type charges are used, differences in atom type charges are moot.<br></font><font size="3">Thus, the effects of these changes are minimal.</font><font size="3"> Curiously, the oplsaa<br>atom type charges from the topolbuild atom type selections appear<br>to be closer to the atom charges given in </font><font size="3">foplsaa.rtp than the </font><font size="3">atom<br>type charges for the oplsaa types used in </font><font size="3">foplsaa.rtp</font><br><font size="3"><br><br>I hope people find this version useful.<br><br><br>Sincerely,<br><br><br></font></div><font size="3"><span style="font-family: times new roman,new
york,times,serif;">-- </span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">Bruce D. Ray, Ph.D.</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">Associate Scientist</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">IUPUI</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">Physics Dept.</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">402 N. Blackford St.</span><br style="font-family: times new roman,new york,times,serif;"><span style="font-family: times new roman,new york,times,serif;">Indianapolis, IN 46202-3273</span></font><div><br></div>
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