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
