Hi Ross and Jason,
Thank you for the clarification. I'll try some awk-foo this week and share my script with the mailing list. (maybe incorporate it into the charmmlipid2amber.x script)
Cheers,
Parker
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Sunday, March 16, 2014 11:29 PM
To: AMBER Mailing List
Subject: Re: [AMBER] tleap lipid residue splitting warnings
Hi Parker,
To follow up on what Jason wrote - this is the expected behavior and the
error message from leap is innocuous and you can ignore it. The issue is
that the Charmm GUI treats each lipid molecule as one residue while
lipid11/14 treat it as 3 residues (allowing it to be modular). The
conversion script updates the residue names but not the numbering so you
have residue 1 repeated 3 times for example and this is what leap is
complaining about. We could fix this, it would just make the conversion
script more complicated since it would have to keep track of residue
numbers rather than just doing a bunch of sed's as it does right now.
Ultimately after leap has read the pdb you can just save a new pdb from
within leap and it should have the correct numbering.
All the best
Ross
On 3/16/14, 9:35 AM, "de Waal, Parker" <Parker.DeWaal.vai.org> wrote:
>Hello Everyone,
>
>I recently tried to set up a membrane bound protein simulation
>(AmberTools version 13.24 Amber version 12.21) following this tutorial ->
>http://scanmail.trustwave.com/?c=129&d=_uum06A70qF21prZQLJ7hFCpgE-A_91QGcuxQochJQ&u=http%3a%2f%2fambermd%2eorg%2ftutorials%2fadvanced%2ftutorial16%2fAn%5fAmber%5fLipid%5fForce%5fFiel
>d_Tutorial.html
>
>Everything seems to work until I try to load the pdb into tleap at which
>point a stream of warnings about split residues appears:
>
>Warning: name change in pdb file residue 1 ;
> this residue is split into OL and PC.
>Warning: name change in pdb file residue 1 ;
> this residue is split into PC and OL.
>...
>
>To check if there was an error in my pdb I also tried to use the
>charmmlipid2amber.x processed DOPC_128_Lipid11.pdb from the tutorial and
>the same warning appears.
>
>Although I can still run a check and saveamberparm without errors is
>there a way to hide these warnings? Or do they mean that there is really
>an error in the pdb input file?
>
>If anyone could provide any insight I'd greatly appreciate it.
>
>Best,
>Parker
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Received on Mon Mar 17 2014 - 08:00:02 PDT
