[gmx-users] X Amino Acids for Building CG Structure

[Tsjerk Wassenaar]

Hi Elka,

Methyl asparagine is not known by DSSP and is not availble in Martini.
You're probably best off replacing it by asparagine:

sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb

Cheers,

Tsjerk

On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda <firmand46 at gmail.com> wrote:

> Hi, I just got "X" amino acids on DSSP, what does it means ? when I use the
> DSSP file to build coarse grained structure with martini 2.2 force field, I
> lost some amino acids because of this "x" amino acids on DSSP. So, how to
> build CG structure if I have this "x" amino acids ? I want to build CG
> structure for phycocyanin (1GH0) chain A-F. The "x" amino acids refers to
> modified residues called "MEN", L-Peptide Linking. Thank you for your help.
>
>
> *Elka Firmanda*
> Graduate Student
> Biophysics Division,
> ​ ​
> Department of Physics
> Faculty of Mathematics and Natural Sciences
> Bogor Agricultural University, Indonesia 16680
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-- 
Tsjerk A. Wassenaar, Ph.D.