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 - 11:00:03 PDT
