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
>>>>
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>>>
>>>
>>>
>>> --
>>> -------------------------
>>> 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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>>
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>
>
>
> --
> -------------------------
> 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
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Received on Wed Aug 30 2017 - 01:30:02 PDT
