Hi Parker,
I'll save you the work since we are currently rewriting the conversion
script in python (which gives us much more functionality). We'll be
releasing this with AmberTools14 shortly.
All the best
Ross
On 3/17/14, 7:52 AM, "de Waal, Parker" <Parker.DeWaal.vai.org> wrote:
>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_91QGc
>>uxQochJQ&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
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://scanmail.trustwave.com/?c=129&d=_-um0wO-OHc9KR85PEqKydxOKgbAPZFKFl
>>UExadkCA&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinfo%2fambe
>>r
>
>
>
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Received on Mon Mar 17 2014 - 09:00:03 PDT
