Re: [AMBER] cannot add bond

From: Elvis Martis <>
Date: Thu, 2 Feb 2017 03:51:04 +0000

Check your atoms names carefully, seems like there is one name given to two atoms.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Thakur, Abhishek []
Sent: Thursday, February 02, 2017 3:56 AM
Subject: [AMBER] cannot add bond


I have been trying to create parameter file for my heteroatom.

I have calculated RESP charges and after that while creating prmtop and inpcrd files I am getting error.

!FATAL ERROR----------------------------------------
!FATAL: In file [unitio.c], line 1810
!FATAL: Message: 1-4: cannot add bond 8 9
This may be caused by duplicate bond specifications; for example, explicit bond commands in addition to PDB conect records.

Everything in structure looks good and connected as expected in mol2 file.

Can anyone suggest me what should I do for this.

With regards,

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Received on Wed Feb 01 2017 - 20:00:02 PST
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