[gmx-users] isoaspartic acid

[Tsjerk Wassenaar]

Hi Andrea,

I would suggest making a building block in the ff*.rtp file. Copy the entry
for aspartic acid, and rearrange such that the connection runs through the
side chain rather than through the backbone.

In addition, you can better use one of the GROMOS force fields, OPLS or
Amber; check posts on the gmx force field (and why not to use it for MD
simulation) in the archive.

Best regards,

Tsjerk

On 2/21/06, andrea spitaleri <spitaleri.andrea at hsr.it> wrote:
>
> Dear all,
> I have a small cyclic peptide (5 aa) and one aminoacid is a non-natural
> aa, isoaspartic acid (isoASP). In order to create a topology file,
> I was thinking to follow to routes:
> 1. create two different itp files, one for standar aa and one for the
> isoASP and then include them in the top file. In this case, how can I
> define the bond between isoASP and the rest of aa in the itp files?
> or
> 2. edit the ffgmx.* files in order to add also this isoASP
> I am not aware of other way to carry out.
>
> Any other suggestions are welcome,
>
> Regards,
>
> andrea
>
>
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> -------------------------------
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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