Hi,
I need to correct myself as I didn't read your previous email with enough care.
You have 120 lipids but they are in a bilayer (which I should not have
missed). Therefore the number of molecules you want to use with
'nmols' is 60, not 120 as I previously stated, since this is the
number of molecules in the XY plane (assuming each leaflet of your
bilayer is 60 lipids).
When you use the mask option cpptraj doesn't assume anything about how
your lipids are arranged, which is why the 'nlayers' option is also
required. So when you are using a mask you need to specify 'nlayers 2'
for a bilayer.
Hope this clears things up,
-Dan
On Wed, Aug 30, 2017 at 4:00 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> and how to define mask properly for the lipid e.g POPC?
> if I use :OL it works good
> but
> :OL,PA,PC calculate wrong area
>
> James
>
> 2017-08-29 21:35 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
>> nmols is the total number of lipid molecules. In this case you have
>> 120 lipids so 'nmols 120'. However, if you're giving cpptraj a mask
>> then you don't need to specify nmols since it will be calculated.
>>
>> -Dan
>>
>> On Wed, Aug 23, 2017 at 9:33 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>> Thanks you!
>>>
>>> Because of the splitting of the lipids on three residues in Lipid14,
>>> should I use it for the following options?
>>>
>>> # calculation of apl for popc bilayer composed of 120 lipids
>>> areapermol OL_area :OL,PA,PC nlayers 2 nmols 60 out apm.dat
>>>
>>> nmols should be provided for 1 leaflet only?
>>>
>>> Thank you!
>>>
>>> James
>>>
>>> 2017-08-21 15:28 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
>>>> Hi,
>>>>
>>>> I recommend just using the 'areapermol' action from cpptraj which
>>>> performs the same procedure in a simpler fashion.
>>>>
>>>> -Dan
>>>>
>>>>
>>>> On Mon, Aug 21, 2017 at 4:19 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>>>> Dear all,
>>>>>
>>>>> there is some problem in the script for calculation of area per lipids
>>>>> following the lipid tutorial.
>>>>>
>>>>>
>>>>> If I have in the cpptraj script the following string:
>>>>>
>>>>> vector test * box out vector.dat
>>>>>
>>>>> I have obtained the error from cpptraj:
>>>>>
>>>>> VECTOR: Type Box, output to vector.dat
>>>>> Error: [vector] Not all arguments handled: [ * ]
>>>>> 1 errors encountered reading input.
>>>>> TIME: Total execution time: 0.2326 seconds.
>>>>>
>>>>> If I have the same string without atom selection:
>>>>> vector test box out vector.dat
>>>>>
>>>>> there is no error.
>>>>>
>>>>> How the syntax should be corrected?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> James
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------
>>>> Daniel R. Roe
>>>> Laboratory of Computational Biology
>>>> National Institutes of Health, NHLBI
>>>> 5635 Fishers Ln, Rm T900
>>>> Rockville MD, 20852
>>>> https://www.lobos.nih.gov/lcb
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 01 2017 - 06:30:04 PDT
