Hi Szymon,
Thanks for pointing that out. Sorry it was wrong in the AMBER manual. It will be fixed in the next release.
Kind regards,
Pengfei
> On Oct 9, 2017, at 3:00 PM, Szymon Żaczek <szymonzaczek.gmail.com> wrote:
>
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 12 2017 - 20:00:03 PDT
