Re: [AMBER] cannot add bond

From: Sowmya Indrakumar <>
Date: Thu, 2 Feb 2017 08:49:20 +0000

Hi Abhishek,
If your already having the conect records for the bonding atoms in your intial PDB file (present in the end of your PDB file) , using bond command again while making the initial parameter file mostly gives such an error.

From: Elvis Martis []
Sent: Thursday, February 02, 2017 4:51 AM
To: AMBER Mailing List
Subject: Re: [AMBER] cannot add bond

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 Thu Feb 02 2017 - 01:00:03 PST
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