[gmx-users] sort_mol2_bonds.pl issue

[Francesco Pietra]

Hi
sort_mol2_bonds.pl (taken from the 2018-updated protein-ligandbtutirial)
does not work for me. The .mol2 file is simply stripped out of the whole
list of bonds, while the atom list remain not ordered (for example oxygen
before carbon). This occurs with also monotone atom numbering. But I also
have cases where atoms are hyphened because of side chains. An excerpt:
1  PB       320.9600  448.8530  308.0120 P.3   501  GDP         0.5373
      2  O1B      320.2560  449.8240  307.0910 O.3   501  GDP        -0.1143
      3  O2B      320.9220  447.3970  307.6090 O.3   501  GDP        -0.1143
      4  O3B      320.6220  449.1260  309.4600 O.2   501  GDP        -0.2221
      5  O3A      322.5080  449.2690  307.8600 O.3   501  GDP        -0.2261
      6  PA       323.6920  448.5990  308.7260 P.3   501  GDP         0.2224
      7  O1A      324.3840  447.6240  307.8010 O.3   501  GDP        -0.4370
      8  O2A      323.1200  447.9850  309.9830 O.2   501  GDP        -0.5170
      9  O5'      324.6580  449.8470  309.1210 O.3   501  GDP        -0.3245
     10  C5'      326.0610  449.8930  308.8080 C.3   501  GDP         0.0836
     11  C4'      326.9510  449.9750  310.0480 C.3   501  GDP         0.1133
     12  O4'      326.8250  448.7650  310.8190 O.3   501  GDP        -0.3456
     13  C3'      328.4210  450.0360  309.6490 C.3   501  GDP         0.1135

Did not find anything about on Internet.
Thanks for advice
francesco pietra