Re: [AMBER] tleap split lipid when it shouldn't

From: Stephan Schott <schottve.hhu.de>
Date: Wed, 15 May 2019 19:42:50 +0200

P.S. I am working on a newer tutorial for membrane systems, which I hope to
have at some point in the next months. I am still fine tuning some things
in packmol-memgen, but if time allows, I will try to explain this things in
there, because is a recurring issue with new "membrane-simulation" users.
If someone else is also working on it, please let me know!

El lun., 13 may. 2019 a las 15:53, David A Case (<david.case.rutgers.edu>)
escribiĆ³:

> On Mon, May 13, 2019, Maximilien BERNE wrote:
> >
> >So i try to make a MD on a protein with a lipid bilayer structure (created
> >with CHARMM-GUI). my lipid is only with DOPC
> >
> >using charmmlipid4amber, to create a file that will change my DOPC into
> >OL and PC. I succed to create the prmtop file and inpcrd . but after
> >simulation i saw that my lipid are still split into three residues and
> >that my bilayer structure is slowly looking like a sphere when the head
> >of the lipid will just float around with water. I know that in force
> >field lipid14 they split DOPC into those 3 residue.
>
> This isn't really an answer to you problem, but a couple of comments
> from an outsider--I hope the lipid experts on this list will chime in with
> corrections or suggestions:
>
> 1. Should the CHARMM-GUI not create Amber files itself? That is, what
> is the need for charmmlipid2amber any more? (The lipid14 tutorial on
> the web page is by now 5 years old....)
>
> 2. The AMBAT or packmol_memgen routines (the latter significantly
> updated in AmberTools19, just released) provides alternative
> Amber-centric methods for creating these systems. See Sections 12.6 and
> 12.7 in the Amber 2019 Reference Manual. That said, tutorials or
> expanded explanations would be most helpful here.
>
> 3. Someone with lipid experience might try to answer the original
> question.
>
> ....regards...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 15 2019 - 11:00:03 PDT
Custom Search