Dear Prof. Ross,
Thanks for your reply, though awaiting for other replies too.
>> Most lipids should be available since you can combine any tail with any head
Ok thanks this clarified further :-) In particular looking for DMPC
>>Do you mean the charmmlipid2amber script does not contain the lipid combination you want? It should >>work with all those offered by the Charmm GUI. What do you need specifically?
I need DMPC actually and I was trying on POPC I get this list of lipids available with charmmlipid2amber::
*** STAGE 4 : STRIP INDIVIDUAL LIPIDS TO SEPARATE FILES ***
Currently supported lipids: DPPC DPPE DPPS DPPG DPPA
DOPC DOPE DOPS DOPG DOPA
POPC POPE POPS POPG POPA
CHL1
DMPC and others are missing??!!! or its just some older message. So I was hesitating to use DMPC!
thanks,
________________________________
From: Ross Walker <ross.rosswalker.co.uk>
To: 'Jio M' <jiomm.yahoo.com>; 'AMBER Mailing List' <amber.ambermd.org>
Sent: Friday, July 13, 2012 7:13 PM
Subject: Re: [AMBER] lipid params
Hi Jio,
> 3) Few lipids are there now in lipid11 (that charmmlipid2amber.x uses).
Most lipids should be available since you can combine any tail with any head
group so I'm not sure I understand what you mean by few lipids are
available. Do you mean the charmmlipid2amber script does not contain the
lipid combination you want? It should work with all those offered by the
Charmm GUI. What do you need specifically?
> As far I was following recent archive mails AMBER will provide params
> which can be used without surface tension once it is published. So the
> params in lipid11 will change after it is published or these are same
> params which can be used without surface tension?
No the parameters will not change for Lipid11. There will be an updated
force field, likely termed lipid12 released most likely with an updated
version of AmberTools.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Jul 13 2012 - 07:30:02 PDT
