Re: [AMBER] frcmod file error

From: Carlos Simmerling <>
Date: Fri, 21 Oct 2016 10:23:25 -0400

We gave you advice before but it seems you keep repeating the same error
and not trying to find out why it is happening. You'll need to look into
your leap logs and see what it says. Sometimes doing research simulations
takes some troubleshooting and testing on your part.

To summarize - making a coordinate file in another program that had a bond
is only part of the process. You also need to explain to leap that it is
cyclic, which prof case already described. If you follow these directions
and still have problems, look into the logs and see if you can find out
why, or tell us why leap is not doing what is expected from the commands
you gave.

On Oct 21, 2016 10:04 AM, "Thakur, Abhishek" <> wrote:

> 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.
> Bill
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Received on Fri Oct 21 2016 - 07:30:04 PDT
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