[AMBER] Wrong number of restrained atoms

From: Valentina Romano <valentina.romano.unibas.ch>
Date: Thu, 3 Jul 2014 09:45:01 +0000

Dear Amber users

I want to run a minimization step keeping frozen a protein-ligand complex and letting free to move water and ions.
My protein-atom complex goes to residue 269 to 525 (2065 atoms).

The input file I used is:

 &cntrl
  imin=1,
  maxcyc=2500,
  ncyc=750,
  ntb=1,
  igb=0,
  ntr=1,
  cut=9.0,
 /
Hold complex fixed
10.0
RES 269 525
END
END

But checking the output file I notice that only 771 atoms are restrained.

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5. REFERENCE ATOM COORDINATES

  defa
    ----- READING GROUP 1; TITLE:
 Hold complex fixed

     GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
 GRP 1 RES 269 TO 525
      Number of atoms in this group = 771
    ----- END OF GROUP READ -----

Why only 771 atoms are restrained and not all?
Someone can help me to understand which is my mistake?

Thanks.
Valentina





~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |

Phone: +41 61 267 15 80


________________________________________
From: Arunima Shilpi [writetoash28.gmail.com]
Sent: Saturday, June 07, 2014 6:48 AM
To: amber.ambermd.org
Subject: [AMBER] error in hydrogen bond

Dear Sir

I executed ptraj command for hbond analysis as follow

 ptraj 3pta_DRG_solvated.top <ptraj_hbond.in >analyse_hbond.out

The ptraj_hbond.in file is as follow

trajin md2.mdcrd

donor mask :905.O5
donor mask :905.OD1
donor mask :905.O7
donor mask :905.O

acceptor mask :454.O :454.H
acceptor mask :475.O :475.H
acceptor mask :905.O :905.H
acceptor mask :882.OD1 :882.H


hbond distance 3.5 angle 120.0 includeself donor mask acceptor mask
neighbor 2 series \ hbond


While running the command i got the following error

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin md2.mdcrd
  Checking coordinates: md2.mdcrd
Rank: 0 Atoms: 187380 FrameSize: 4553359 TitleSize: 81 NumBox: 3 Seekable 1


PTRAJ: donor mask :905.O5
Mask [:905.O5] represents 1 atoms

PTRAJ: donor mask :905.OD1
Mask [:905.OD1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:905.OD1), ignoring...

PTRAJ: donor mask :905.O7
Mask [:905.O7] represents 1 atoms

PTRAJ: donor mask :905.O
Mask [:905.O] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:905.O), ignoring...

PTRAJ: acceptor mask :454.O :454.H
Mask [:454.O] represents 1 atoms
Mask [:454.H] represents 1 atoms

PTRAJ: acceptor mask :475.O :475.H
Mask [:475.O] represents 1 atoms
Mask [:475.H] represents 1 atoms

PTRAJ: acceptor mask :905.O :905.H
Mask [:905.O] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:905.H] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No heavy atom was selected (:905.O), ignoring...
WARNING in ptraj, acceptor: No hydrogen atom was selected (:905.H),
ignoring...

PTRAJ: acceptor mask :882.OD1 :882.H
Mask [:882.OD1] represents 1 atoms
Mask [:882.H] represents 1 atoms

PTRAJ: hbond distance 3.5 angle 120.0 includeself donor mask acceptor mask
neighbor 2 series \ hbond[No output trajectory specified (trajout)]
  md2.mdcrd: 5000 frames.

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 5000 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (md2.mdcrd) is an AMBER trajectory (with box info) with 5000 sets

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
  1> HBOND saved to series \, inter-solvent hbonds will not be included,

      data will be sorted, intra-residue interactions will be included,
      Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information will be dumped for occupancies > 0.00
      Estimated memory usage for this hbond call: 0.34 MB
      donors: 2 acceptors: 3 frames: 5000



Processing AMBER trajectory file md2.mdcrd

 1% ............ 25% ............ 50% ............ 75% ............ 100%


PTRAJ: Successfully read in 5000 sets and processed 5000 sets.

Dumping accumulated results (if any)

  HBOND SUMMARY:
      Data was saved to series \,
      data was sorted, intra-residue interactions are included,
      Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
      Hydrogen bond information dumped for occupancies > 0.00

  Dumping schematic of time series after each h-bond, key follows:
   | . - o x * . |
      0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy

        DONOR ACCEPTORH ACCEPTOR
  atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance
  angle lifetime maxocc
 ---------------- ---------------------------------
-------------------------------------
 Kindly guide in debugging the error.

Regards

Arunima
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Received on Thu Jul 03 2014 - 03:00:02 PDT
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