hello Ben:
I try the link you gave me and I installed that tools under
AmberTools1.5 since it tool only support AT1.5 currently. here is my
input file for ptraj:
trajin md.mdcrd 1 50000 100
vector POPE :314-679 corrplane out pope.vector
and here is that I got:
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" modified Aug 12 2011 by HH
Loeffler, STFC Daresbury
-/- Executable is: "/opt/amber11/AmberTools/src/ptraj.mod/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
ACE VAL SER ASP TYR VAL ASN TYR ASP ILE
ILE VAL ARG HIE TYR ASN TYR THR GLY LYS
PE OL PA PE OL PA PE OL PA PE
OL PA PE OL PA PE OL PA PE OL
PA PE OL PA PE OL PA PE OL Cl-
Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl-
...
K+ K+ K+ K+ K+ K+ K+ K+ K+ K+
...
K+ WAT WAT WAT WAT WAT WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT WAT
PTRAJ: Processing input from file md.mdcrd
PTRAJ: default_name
PTRAJ: 34.467 17.494 93.162 33.625 16.848 92.912 32.706 17.039
93.466 33.929
PTRAJ: 15.848 93.222 33.348 16.884 91.427 33.426 15.844 90.816
32.925 17.990
PTRAJ: 90.864 32.671 18.698 91.538 32.956 18.303 89.428 32.403
19.243 89.436
PTRAJ: 34.407 18.591 88.829 35.051 18.829 89.676 34.995 17.342
88.123 36.076
PTRAJ: 17.456 88.048 34.806 16.491 88.778 34.426 16.986 87.263
34.364 19.681
PTRAJ: 87.785 35.327 19.657 87.277 33.547 19.542 87.077 34.272
20.710 88.135
PTRAJ: 31.941 17.498 88.502 31.667 17.967 87.389 31.361 16.424
89.036 31.909
PTRAJ: 16.115 89.827 30.448 15.551 88.268 30.877 15.389 87.279
30.336 14.179
PTRAJ: 88.874 29.436 13.705 88.483 31.278 13.709 88.590 30.335
14.165 90.274
PTRAJ: 29.947 13.360 90.624 29.101 16.208 88.021 28.144 15.592
87.605 28.855
PTRAJ: 17.469 88.412 29.614 18.065 88.710 27.559 18.151 88.146
26.759 17.415
PTRAJ: 88.221 27.233 19.136 89.299 26.303 19.689 89.164 27.144
18.466 90.155
.....
Do you have any idea which number is area/lipids?
I also try AmberTools12 with above command, but it said:
Warning: Output of corr, ired, corrired or corrplane vectors is not yet
supported!
here is the full log files:
PTRAJ: vector POPE :314-679 corrplane out pope.vector
Mask [:314-679] represents 15250 atoms
[No output trajectory specified (trajout)]
md.mdcrd: 50000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 500 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (md.mdcrd) is an AMBER trajectory (with box info) with 50000
sets (processing only 500)
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> VECTOR: storage to array named POPE
Calculate the vector perpendicular to the least squares best plane
through the atom selection which follows
Atom selection is :314-679
The order of Legendre polynomials is 2
Warning: Output of corr, ired, corrired or corrplane vectors is
not yet supported!
Processing AMBER trajectory file md.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
PTRAJ: Successfully read in 500 sets and processed 500 sets.
Dumping accumulated results (if any)
And I don't get any new generated file.
thank you very much
best
Albert
On 06/18/2012 08:25 PM, Benjamin D Madej wrote:
> Yes, we primarily use ptraj scripts to do the calculations. That web site is a good resource. I'll repost the link:
> http://www.stfc.ac.uk/cse/25249.aspx
>
> One of our collaborators actually contacted that author to see if they wanted to include their code in the official releases of ptraj, but I don't know what the response was. It'd be nice to include in Amber.
>
> The ptraj 'vector' command can give you the x and y dimension from which you can calculate the box area.
>
> Ben
>
> On Jun 18, 2012, at 11:16, "Albert"<mailmd2011.gmail.com> wrote:
>
>> hello Benjamin:
>>
>> thank you for kind comments.
>>
>>
>> On 06/18/2012 06:28 PM, Benjamin D Madej wrote:
>>> Hello Albert,
>>>
>>> 50ns may not be long enough to converge just your POPE bilayer. Are you able to show the area per lipid vs. time for your simulation?
>>>
>>> The first screenshot qualitatively looks too ordered. But I can't tell with the second and third.
>>>
>>> Are you actually calculating an order parameter for your acyl tails? It's fairly common to compare this to experimental order parameter values.
>>>>>> I would like to. However, I don't know how to do this in Amber. I
>> look through the whole Amber 12 and AmberTools 12 user guide and don't
>> find any comments on this. If possible, would you please have some
>> comment on how to do this ?
>>
>>
>>> Please see my previous comments about the overly ordered saturated acyl chains in Lipid11.
>> yes, I saw that days ago
>> /
>> "/
>>
>> /The saturated acyl tail order is an issue we have been working on, and we are currently testing new parameters for their effect on the tail order and on the bilayer structural properties. We'd like to avoid the artificial constant surface tension all together with a parameter set that can run MD with the tensionless NPT ensemble./
>>
>> /"
>> /
>>
>>> It is possible to extract area per lipid using ptraj. There is a command 'vector' that will output the periodic box dimensions.
>>>>> I tried to do this by command 'ptraj'
>> \-/
>> -/- PTRAJ: a utility for processing trajectory files
>> /-\
>> \-/ Version: "AMBER 12.0 integrated" (4/2012)
>> -/- Executable is: "ptraj"
>> /-\ Running on 1 processor(s)
>> \-/ Input the name of an AMBER prmtop, CHARMM PSF or PDB file:
>> POPE.prmtop
>> Opened file "apo.prmtop" with mode (r)
>> Residue labels:
>> PA PE OL PA PE OL PA PE OL PA
>> PE OL PA PE OL PA PE OL PA PE
>> OL PA PE OL PA PE OL PA PE OL
>> PA PE OL PA PE OL PA PE OL PA
>> PE OL PA PE OL PA PE OL PA PE
>> OL PA PE OL PA PE OL PA PE OL
>> PA PE OL PA PE OL PA PE OL PA
>> PE OL PA PE OL PA PE OL PA PE
>> ....
>> PTRAJ: Processing input from "STDIN" ...
>>
>> then it stack there and I don't get any additional dialogue for
>> specifying the trajectories.
>>
>>
>>> Also, surely the protein and the relative number of lipids will play a role in your membrane bound protein system.
>> This system contains a protein with around 300 aa protein and 128 POPE
>> lipids which should be reasonable for general membrane protein simulations.
>>
>> thanks again for your kind comments.
>>
>> best
>> Albert
>>
>>
>>> Ben
>>> Walker Molecular Dynamics Lab
>>>
>>> On Jun 18, 2012, at 7:10, "Albert"<mailmd2011.gmail.com> wrote:
>>>
>>>> hello:
>>>>
>>>> I am using the following parameters for lipid 11 FF POPE study:
>>>>
>>>> equilibration
>>>> &cntrl
>>>> imin=0, irest=1, ntx=5,
>>>> nstlim=25000000, dt=0.002,
>>>> ntc=2, ntf=2,
>>>> cut=10.0, ntb=2, ntp=3, taup=2.0,
>>>> ntpr=5000, ntwx=5000, ntwr=50000,
>>>> ntt=1,
>>>> iwrap=1,
>>>> temp0=310.0,
>>>> csurften=3, ninterface=2,gamma_ten=26,
>>>> /
>>>>
>>>> and I did two test:
>>>>
>>>> 1. 50ns for pre-equilibrated POPE (40ns under CHARMM36)
>>>> 2. 100 ns for protein/POPE (POPE also equilibrated for 40ns under CHARMM36)
>>>>
>>>> what I found is that for both cases, the POPE are too 'ordered' and it
>>>> has some preference for origination. Does any body have any idea what
>>>> happen to those lipids.
>>>>
>>>> here are three screenshot from VMD for above mentions.
>>>>
>>>> https://dl.dropbox.com/u/56271062/f/1.jpg
>>>> https://dl.dropbox.com/u/56271062/f/2a.jpg
>>>> https://dl.dropbox.com/u/56271062/f/2b.jpg
>>>>
>>>>
>>>> BTW, does anybody knows how to calculate area/lipids in Amber so that we
>>>> know whether our system is reliable or not?
>>>>
>>>> thank you very much
>>>> Albert
>>>>
>>>>
>>>>
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Received on Tue Jun 19 2012 - 05:30:02 PDT
