Hi,
It seems like there is an extra conect entry in your pdb file which is trying make an unusually long bond. Please see your ligand structure in leap to see what is wrong.
You can delete this bond in leap itself and see if you can save your prmtop and inpcrd files.
Hope this helps.
Best Regards
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Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
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________________________________
From: NADIA RAHMAH <nadiiarah.apps.ipb.ac.id>
Sent: 28 May 2017 16:29:59
To: amber.ambermd.org
Subject: [AMBER] Fwd: Error while preparing docked complex for minimization
Hello, I am doing AMBER16 for simulating docked complex protein, but there
is error while preparation:
WARNING: There is a bond of 3.687021 angstroms between:
------- .R<UNL 295>.A<C 1> and .R<UNL 295>.A<O 2>
FATAL: Atom .R<UNL 295>.A<BR 9> does not have a type.
Failed to generate parameters
Parameter file was not saved.
my ligand name unl, before i do peparation for complex, i did antechamber
for the ligand and get unl.lib, unl.frcmod that i use for loadamberparams
in preparation script but i still get error when preparation complex. I
need to fix it, because it's my undergraduate thesis, i hope anybody can
help me. Thanks
--
*Regards,*
*Nadia Rahmah*
*Department of Physics Undergraduate Student - 2013Bogor Agricultural
University*
--
*Regards,*
*Nadia Rahmah*
*Department of Physics Undergraduate Student - 2013Bogor Agricultural
University*
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Received on Sun May 28 2017 - 05:00:02 PDT
