Re: AW: Aromatic rings don't maintain the planarity during the heating

From: Serena Vittorio (svittorio_at_unime.it)
Date: Fri May 04 2018 - 11:51:39 CDT

Thanks for your answer. I don't get any conformation like in sugar, but only flapping around as you said.
Best regards
----- Messaggio originale -----
Da: Daniel Möller <daniel.moeller3_at_uni-greifswald.de>
A: namd-l_at_ks.uiuc.edu, 'Serena Vittorio' <svittorio_at_unime.it>
Inviato: Fri, 04 May 2018 18:23:24 +0200 (CEST)
Oggetto: AW: namd-l: Aromatic rings don't maintain the planarity during the heating

Hi,

what do you mean with “distorted“? How much?

Cause a little “flapping” around is normal even in aromatic rings.

But if you get some conformation like in sugar ("chair" and "boat" conformation), then something is wrong.

 

Sincerely

 

Daniel Möller

 

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Serena Vittorio
Gesendet: Freitag, 4. Mai 2018 18:15
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Aromatic rings don't maintain the planarity during the heating

 

Dear NAMD users,

I'm applying MD simulation to a protein-peptide system. During the heating I found that the aromatic rings of the aromatic residues of all the system are distorted, they don't maintain the planarity.

Does anyone know which could be the reason?

 

Before the heating I ran two steps of minimization, each one for 1000 steps: the first one with the proteins fixed to relax water molecules and the second one with the C alpha fixed. I heated up the system to 300K for 500 ps.

I attached the namd configuration file referred to the heating.

 

Thanks,

Serena

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