Re: [AMBER] issue - add_bonded_pairs

From: Miha Purg <>
Date: Mon, 9 Oct 2017 17:53:04 +0000

Hi Szymon,

I believe the indexes must be separated by a dash, with two indexes per line.


add_bonded_pairs 3927-3930

add_bonded_pairs 3927-3931

Hope this helps.



From: Szymon Żaczek <>
Sent: Monday, October 9, 2017 5:37:38 PM
To: AMBER Mailing List
Subject: [AMBER] 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
( 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 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 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/", 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 ignores coordinating carbon atoms).

So either I am missing something very obvious here, or there is an
error within 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
Received on Mon Oct 09 2017 - 11:00:03 PDT
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