Dear Miha,
thank you very much for your help - the fix you proposed works perfectly.
By the way, I would recommend including this fix in the next version
of Amber manual, since the information included therein about
specifying bonded pairs in MCPB.py are not correct.
Kind regards,
Szymon Żaczek
2017-10-09 19:53 GMT+02:00 Miha Purg <miha.purg.icm.uu.se>:
> Hi Szymon,
>
>
> I believe the indexes must be separated by a dash, with two indexes per line.
>
> E.g.
>
> add_bonded_pairs 3927-3930
>
> add_bonded_pairs 3927-3931
>
>
> Hope this helps.
>
>
> Cheers,
>
> Miha
>
> ________________________________
> From: Szymon Żaczek <szymonzaczek.gmail.com>
> Sent: Monday, October 9, 2017 5:37:38 PM
> To: AMBER Mailing List
> Subject: [AMBER] MCPB.py issue - add_bonded_pairs
>
> Dear Amber developers,
>
> I want to obtain force field bonds and angles parameters for Ruthenium
> ion that is being a part of a metallocene molecule
> (https://en.wikipedia.org/wiki/Metallocene). Those compounds consist
> of a metal that is being coordinated by 10 carbon atoms, therefore, as
> it is stated in Amber manual, "add_bonded_pairs" instruction must be
> specified in MCPB.py input file during first step, since only
> Metal-N/O/S/F/Cl/Br/I bonds are originally detected by the program.
>
> Here is my MCPB.py input file:
>
> original_pdb 5ujo_ready.pdb
> group_name metal
> cut_off 2.5
> ion_ids 3927
> add_bonded_pairs 3927 3930 3927 3931 3927 3932 3927 3933 3927 3935
> 3927 3939 3927 3940 3927 3941 3927 3942 3927 3943
> ion_mol2files RU.mol2
> naa_mol2files 8CY.mol2
> frcmod_files 8CY.frcmod
> large_opt 1
> software_version g09
>
> The error message I have received after executing the files as step one:
>
> Traceback (most recent call last):
> File "/net/software/local/amber/amber16/bin/MCPB.py", line 176, in <module>
> raise pymsmtError('Should be only two numbers in the pairs!')
> pymsmtexp.pymsmtError: Should be only two numbers in the pairs!
>
> Deleting all of the bonded pairs except the first one (3927 3930)
> produces the same error. However, when I delete 'add_bonded_pairs'
> line entirely, the program succeds in creating Gaussian input files,
> though they contain only Ruthenium ion (what is correct since by the
> default MCPB.py ignores coordinating carbon atoms).
>
> So either I am missing something very obvious here, or there is an
> error within MCPB.py code itself.
>
> Would you mind help me resolving this issue?
>
> I attach to this email all of the related files.
>
> Kind regards,
> Szymon Żaczek
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Received on Mon Oct 09 2017 - 13:30:02 PDT
