The P4 is correct, the phosphorous has three different substituents
attached, the two oxygens which are attached to the phosphorous are
equivalent.
On 13/07/2012 10:10, "Jio M" <jiomm.yahoo.com> wrote:
>Hi,
>
>thanks for nice suggestions,
>
>
>>> Just ensure that the ff parameters are kept as in the original paper
>>>even if you need to change the name of the atom type.
>
>
>the paper I mentioned was in 2008, at that time I think p5 atom type was
>available, but they still used p4!
>
>and also can you please suggest something any reason regarding "S"
>configuration they used.
>
>CHARMM GUI provides R lipids. But Also I cant find standard paper
>reference saying lipids exist in R or S form so they should be used for
>simulations. Just using R or S blindly looses the importance of
>stereochemitry we learnt in Junior schools :-)
>
>
>
>________________________________
> From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
>To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>Sent: Friday, July 13, 2012 2:23 PM
>Subject: Re: [AMBER] lipid params
>
>Without being a major expert ...
>
>My feeling at the moment is that for many questions you can safely use
>gaff parameters with appropriate surface tension (lipid11 should be
>similar, home I am not sayoing something wrong, did not work with
>lipid11 yet). Just monitor during the simulations some properties of the
>membrane and make sure that you are in the range of experimental values.
>If you are looking for the perfect membrane, you need to take a good
>look at the literature describing the effects of surface tension in
>lipid simulations or you might need to switch to CHARMM36 (which might
>not be perfect either, but seems to be best lipid ff described thus far).
>
>The names of atom types might need adaptation as with new versions of
>force fields names can overlap and you might need to take care of that.
>Just ensure that the ff parameters are kept as in the original paper
>even if you need to change the name of the atom type.
>
>As for the lipid11 without surface tension, I believe the best strategy
>is to wait for the publications and see how well it does. Of course,
>unless you have the time to do long tests and then you could ask the
>developers to share with you the modifications for testing purposes (of
>course its up to them whether they share at the moment or they also
>prefer to wait until publication).
>
>Best
>Vlad
>
>
>On 07/13/2012 10:35 AM, Jio M wrote:
>> Dear All,
>>
>>
>> {Sorry for long mail}
>>
>>
>> As lipids are hot now these days on AMBER archive, I was trying to do
>>some simulations on DMPC, which still I think not there in AT12 (that
>>charmmlipid2amber.x supports conversion). So instead I tried using DMPC
>>gaff params by Gould et al.'s J. Comput. Chem. Vol 29, page 24-37. But I
>>have some doubts:
>>
>> 1) The atom type used for Phosphorous is p4 (gaff), which is actually
>>should be p5. To recall the things, p4 type is for P attached to three
>>atoms, while p5 is used for P with four atoms. What can be the reason?,
>>I wonder to choose p4 as I see there is much difference in the bond,
>>angles and torsional terms though compared to p5, vdw remains same.
>>
>> 2) Secondly the paper uses and validate many things with "S"
>>configuration DMPC bilayer (the single residue is in "S" configuration,
>>as provided in Richard's Bryce website). So can I assume these
>>validations remain same for "R" configurations as DMPC lipid is R (I
>>dont have reference for that though, but what CHARMM-GUI provides and
>>other lipids are in R form only.). So is there any special reason 'S'
>>lipid was used in such study? Anyhow I can use params for R also.
>>
>> 3) Few lipids are there now in lipid11 (that charmmlipid2amber.x uses).
>>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?
>>
>>
>> regards,
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>--
>Dr. Vlad Cojocaru
>Max Planck Institute for Molecular Biomedicine
>Department of Cell and Developmental Biology
>Röntgenstrasse 20, 48149 Münster, Germany
>Tel: +49-251-70365-324; Fax: +49-251-70365-399
>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>
>
>
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Received on Fri Jul 13 2012 - 02:30:02 PDT
