Re: [AMBER] How Can I modify a amino acid in Amber

From: Changqing Yan <>
Date: Mon, 22 Oct 2012 10:22:19 +0800

Dear Francois,

Thanks a lot for your last reply. I have completed some steps according to
your instruction. However, when I was going to run REDServer using P2N file
and QM optmization file, it goes wrong with the log file displaying "

        * Selected optimization output *
              Invalid optimization OUTPUT !

    The atom order in the P2N file and QM output are not compatible

What 's wrong with this? How can I fix it?

FYI, my opt card is " #P rhf/6-31g* Pop=MK iop(6/33=2) opt". My pdb file
was formed from opt output file using Gaussianview5. And the P2N file was
generated using RED IV from that pdb file.

Thanks and best regards,


Message: 7
Date: Mon, 15 Oct 2012 07:22:59 +0200
From: FyD <>
Subject: Re: [AMBER] How Can I modify a amino acid in Amber?
To: AMBER Mailing List <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";

Dear Changqing Yan,

> Thanks for your answers. I am now trying to understand it and making my
> non-standard residue. However, as a rookie, I still need to learn much
> things. Could anyone teach me step by step how to built such as
> cyclo(PSPF(N-methyl)V)? The valanine residue is methylated.

If I understand you, you have a cyclopeptide with a N-methylated
valine. Right?

If so, you need to start by creating the dipeptide of this
N-methylated valine; i.e. create the PDB file for:
here you need to decide which conformation(s) you want to use in
charge derivation and FF library building.

Then, you use R.E.D. Server/Ante_R.E.D. 2.0 to generate the P2N file
starting from the PDB file.

At this point you need to add in the P2N file the charge constraints
that leads to the central fragment of this N-methylated valine:
You have to set 2 intra-molecular charge constraints (INTRA-MCC
keyword) set to zero.


       Whole molecule Fragment
   <---> <--->
    2 intra-mcc = 0

Finally you run R.E.D. III.x or R.E.D. Server/R.E.D. IV to get the
mol2 file for the NMeCHRCO fragment than can be included in your

You could decide to generate with this central fragment, the
N-terminal & C-terminal (although they are not needed _if_ you want to
study a clycopeptide):

These 3 fragments can now be automatically generated using R.E.D. Server:

regards, Francois
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Received on Sun Oct 21 2012 - 19:30:10 PDT
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