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
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Received on Tue Aug 29 2017 - 13:00:03 PDT
