Thank you Dan,
Most helpful. Grateful as ever
George
> On 20 Sep 2017, at 18:26, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> If your intention is to look for peaks which you can use as input for
> 'spam' you probably want to use an 'rms' command to remove
> translation/rotation from your solute of interest, then 'center' to
> ensure your system is centered on the grid, i.e. you want the system
> oriented such that the solute is your reference frame. Otherwise with
> the overall translational motion present in your system it is entirely
> possible for there to be no solvent peaks.
>
> For example (assuming residues 1-125 are the solute):
>
> rms first :1-125
> center :1-125 mass origin
> volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size
> 5,5,5peakcut 0.001 peakfile peaks
>
> Hope this helps.
>
> -Dan
>
> On Fri, Sep 15, 2017 at 9:54 AM, George Tzotzos <gtzotzos.me.com> wrote:
>> I’m running cpptraj volmap to generate a peakfile for subsequent SPAM analysis. The solvent is water.
>>
>> The cpptraj volmap.in file that I used is:
>>
>> volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size 5,5,5 center -54.5,-13.5,-18.5 peakcut 0.01 peakfile peaks
>>
>> I assume the grid size (5,5,5) is in angstrom along the X,Y,Z dimensions. Is it legitimate instead of the center argument above to use centermask :1-125?
>>
>> In either case the generated peakfile contained no data, even at a very small peakcut (0.001).
>>
>> Thank you in advance for any suggestions
>>
>> George
>>
>> INPUT: Reading input from 'volmap.in'
>> [parm subA_solv.prmtop]
>> Reading 'subA_solv.prmtop' as Amber Topology
>> Radius Set: H(N)-modified Bondi radii (mbondi2)
>> [trajin prod_100ns.nc]
>> Reading 'prod_100ns.nc' as Amber NetCDF
>> [volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size 5,5,5 centermask :1-125 peakcut 0.001 peakfile peaks]
>> VOLMAP: Grid spacing will be 0.50x0.50x0.50 Angstroms
>> Grid centered at origin.
>> Gridding atoms in mask ':WAT.O'
>> Dividing radii by 1.360000
>> Density will wrtten to 'volmap.xplor'
>> Grid dataset name is 'GRID'
>> Density peaks above 0.001 will be printed to peaks in XYZ-format
>> [run]
>> ---------- RUN BEGIN -------------------------------------------------
>>
>> PARAMETER FILES (1 total):
>> 0: subA_solv.prmtop, 13140 atoms, 3847 res, box: Trunc. Oct., 3723 mol, 3713 solvent
>>
>> INPUT TRAJECTORIES (1 total):
>> 0: 'prod_100ns.nc' is a NetCDF AMBER trajectory, Parm subA_solv.prmtop (Trunc. Oct. box) (reading 10000 of 10000)
>> Coordinate processing will occur on 10000 frames.
>>
>> BEGIN TRAJECTORY PROCESSING:
>> .....................................................
>> ACTION SETUP FOR PARM 'subA_solv.prmtop' (1 actions):
>> 0: [volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.36 name GRID size 5,5,5 centermask :1-125 peakcut 0.001 peakfile peaks]
>> Volmap: Grid mask [:WAT.O] selects 3713 atoms.
>> ----- prod_100ns.nc (1-10000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> Read 10000 frames and processed 10000 frames.
>> TIME: Avg. throughput= 3651.9995 frames / second.
>>
>> ACTION OUTPUT:
>> No peaks found with a density greater than 0.001
>>
>> DATASETS (1 total):
>> GRID "GRID" (float grid), size is 1000
>>
>> DATAFILES (2 total):
>> volmap.xplor (Xplor File): GRID
>> peaks (Volmap Peaks)
>>
>> _______________________________________________
>> 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 Wed Sep 20 2017 - 12:00:04 PDT
