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

From: FyD <>
Date: Mon, 22 Oct 2012 07:59:59 +0200

Dear Changqing Yan,

> 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 "

Please, provide the R.E.D. Server job name "PXXX" so that we can have
a look to your problem.

> * 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?

When using R.E.D. Server/R.E.D. IV in its mode 2 (See the atom
order in the P2N
  file and in the QM output provided as input to R.E.D. Server/R.E.D.
IV have to be identical.

> 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.

R.E.D. differentiates the two QM steps; i.e. (i) geometry optimization
and (ii) MEP computation. This allows rigorously controlling the
orientation of the optimized geometry before step (ii) and this leads
to reproducible MEP-based charge values.

For geometry optimization, I would rather use #P rhf/6-31g* Opt=Tight.
or just run R.E.D. Server/R.E.D. IV in its Mode 1; i.e. providing only
the P2N file.

regards, Francois

> Dear Changqing Yan,
>> Thanks for your answers. I am now trying to understand it and making my
> own
>> non-standard residue. However, as a rookie, I still need to learn much
> 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.
> See
> 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
> cyclopeptide.
> 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

AMBER mailing list
Received on Sun Oct 21 2012 - 23:30:02 PDT
Custom Search