Re: [AMBER] CUDA and Restraint Error

From: Mehreen Ghufran <mehreen.awkum.edu.pk>
Date: Sat, 5 Jan 2019 22:08:01 +0500

(no subject)
M
Mehreen Ghufran
to ASHFAQ
2 days ago
Details
Hello
kindly check the below error.
linux-njex:/home/awd/9peptide/9 # cpptraj -p complex-water.prmtop -i pca2.in


CPPTRAJ: Trajectory Analysis. V18.00
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_

| Date/time: 01/03/19 10:54:26
| Available memory: 25.008 GB

        Reading 'complex-water.prmtop' as Amber Topology
        Radius Set: H(N)-modified Bondi radii (mbondi2)
INPUT: Reading input from 'pca2.in'
  [reference complex-water.inpcrd]
        Reading 'complex-water.inpcrd' as Amber Restart
        Setting active reference for distance-based masks:
'complex-water.inpcrd'
  [trajin combine.mdcrd 1 last 5]
        Reading 'combine.mdcrd' as Amber Trajectory
  [strip :WAT:Na+:Cl-]
    STRIP: Stripping atoms in mask [:WAT:Na+:Cl-]
  [strip .H=]
    STRIP: Stripping atoms in mask [.H*]
  [autoimage]
    AUTOIMAGE: To box center based on center of mass, anchor is first
molecule.
  [rms reference .CA]
    RMSD: (.CA), reference is "default_name" (@CA).
        Best-fit RMSD will be calculated, coords will be rotated and
translated.
  [matrix covar !.H= matrixstack byatom analyze matrix matrixstack out
kras9_matrix.analyse_output.txt vecs 10]
    MATRIX: Calculating covariance matrix, output is by atom.
        Printing to file kras9_matrix.analyse_output.txt
        Matrix data set is 'Mat_00003'
        Start: 1 Stop: Final frame
        Mask1 is '!.H*'
Error: [matrix] Not all arguments handled: [ matrixstack analyze matrix
matrixstack vecs 10 ]
        1 errors encountered reading input.
Warning: Set 'Mat_00003' contains no data.
Warning: File 'kras9_matrix.analyse_output.txt' has no sets containing data.
TIME: Total execution time: 0.1554 seconds.
Error: Error(s) occurred during execution.n Saturday, January 5, 2019,
Pratul Agarwal <pratul.agarwal-lab.org> wrote:

> update.7 for AMBER v18 addresses this problem. I am not sure if there is a
> patch for v16 to fix this issue, somebody from the GPU code developers team
> will need to confirm.
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
>
>
> On 1/5/2019 9:40 AM, David Case wrote:
>
> On Fri, Jan 04, 2019, Kung, Ryan wrote:
>
>
>
> I am having trouble running restrained MD simulation with pmemd.cuda on
>
> and my restraint file is:
>
> &rst iat=-1,-1, r1=18.6, r2=28.6, r3=28.6, r4=38.6, rk2=10., rk3=10.,
> ir6=0, ialtd=0, iresid=0, igr1=6229,6251,6252,6231,6294,6296,
> igr2=9515,9516,9519, /
> /
>
>
>
> Just to be sure: have you installed all updates, especially update.7,
> which addresses problems in using COM restraints in pmemd.cuda? Go
> to $AMBERHOME, and type "./update_amber --help" for information, and
> "./update_amber --update" to get your code up to date. Then, re-run
> configure and make.
>
> ....dac
>
>
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Received on Sat Jan 05 2019 - 09:30:03 PST
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