Re: [AMBER] frcmod file error

From: Thakur, Abhishek <>
Date: Fri, 21 Oct 2016 14:02:57 +0000

Hi I have managed to make it cyclic by making bond in gaussian.

But as soon as I am solvating it and making prmtop, inpcrd and pdb it seems that N terminal is breaking bond and making it -NH3

I don't know why it is creating so much of trouble.

From: Bill Ross <>
Sent: Friday, October 21, 2016 1:43:38 AM
To:; AMBER Mailing List
Subject: Re: [AMBER] frcmod file error

>> 3. generate a reasonable starting structure for the cyclized peptide.
> Amber is not a very good tool (generally speaking) for carrying out step 3.
Though not the best at it, xleap will let you construct a cyclic
peptide. In the cmd line:

> mymol = sequence { ALA ALA .. ALA } # not a chemist btw
> edit mymol

And there get used to the controls so you can select the end atoms of
the linear molecule one by one and and crudely move each out of line, so
that you can draw a long bond between those atoms. Then select all the
atoms, relax selection, all the weird bonds will be fixed as the
molecule reforms, and with luck you are done, though iterative
selection/relaxation might be needed if kinks develop. The energy
minimization function is based on atom hybridizations, and lacks vdw.

In the end you might want to have a more powerful and used molecular
editor program at your fingertips, but xleap is there and once upon a
time we put some time into making it work.


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