Re: [AMBER] frcmod file error

From: Thakur, Abhishek <>
Date: Fri, 21 Oct 2016 14:25:16 +0000

Hi Dr.Carlos,

Can it be a reason that while building structure I have determined N and C terminal.

So amber is considering N and C terminal and not allowing it to bond.

So when manually I make it somewhere in pdb it has information of being N and C terminal and it is assigning things that way and not making bond?

Can there be a way by which I can make a structure withouth determining N and C terminal?

From: Carlos Simmerling <>
Sent: Friday, October 21, 2016 3:19:48 AM
To: AMBER Mailing List
Cc: David A Case
Subject: Re: [AMBER] frcmod file error

While this works, in my experience it nearly always ends up inverting
chiralities or flipping amides, or sometimes putting bonds through the
middle of rings. I mentioned this in a previous version of this thread, it
seems we are starting to repeat things.

On Oct 21, 2016 8:43 AM, "Bill Ross" <> wrote:

> >> 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.
> Bill
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Received on Fri Oct 21 2016 - 07:30:05 PDT
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