Hi Gerald,
Thank you for reply. I have generated through antechamber.Yes there are several repetition in BOND section as:
1) 10 4 5 1
11 4 5 1
2) 28 12 23 1
29 12 23 1
3) 49 20 21 1
50 20 21 1
4) 54 24 25 1
55 24 25 1
Should I edit this manually (like remove them) ???
Thanks,Hira
On Tuesday, September 3, 2019, 02:17:31 PM GMT+1, Gerald Monard <Gerald.Monard.univ-lorraine.fr> wrote:
Hello Hira,
There is a problem in your .mol2 file: in the BOND section, there are
two lines (10 and 11) that describe the same bond between atom 4 and
atom 5. I guess that this .mol2 file was not generated correctly. Check
your procedure and recreate this .mol2 file, that should correct your
problem.
Best,
Gerald.
On 9/3/19 12:56, Hira Jabeen wrote:
> Hi everyone,
> I am parameterizing a small ligand in Amber 18 with ambertools19.
> On saving parameters, I get the following error:
>> saveamberparm MEM MEM.prmtop MEM.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [unitio.c], line 1810
> !FATAL: Message: 1-4: cannot add bond 4 5
> This may be caused by duplicate bond specifications;
> for example, explicit bond commands in addition to PDB conect records.
> !
> !ABORTING.
> Ligand and leap files are attached.Need your advice.
> Thanks,Hira
>
>
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Received on Tue Sep 03 2019 - 09:00:02 PDT
