[gmx-users] sort_mol2_bonds.pl issues

[Justin Lemkul]

On 11/26/18 2:46 AM, Francesco Pietra wrote:
> Hi
> sort_mol2_bonds.pl (taken from the 2018-updated protein-ligandb tutorial)
> 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, or C13 before C1). This occurs with also monotone atom
> numbering. But I also have cases with also hyphenated due to the presence
> of side chains. An excerpt from the universal GDP
> 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.

Please send me your .mol2 file off-list. The script doesn't do anything 
to the atoms, only the bonds, so I can't tell what's going on. As this 
is not a GROMACS problem, please just contact me directly about the issue.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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