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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Wed, 21 Jun 2017 09:23:31 -0400

Hi,

The standard deviation for hydrogen bond distance and angle are not

currently tracked. It has been requested enough times that I'll

probably implement it at some point. I've added it to my 'hbond' to-do

list here: https://github.com/Amber-MD/cpptraj/issues/392

You can get this information with cpptraj as it is now but it takes a

few steps. You have to:

1) Make sure you record the time series data for hydrogen bonds

('series' keyword) and write it to a file ('uuseries' or 'uvseries').

2) In a separate run, use that data along with the 'filter' command to

save the atoms you will use to calculate the distance only for the

frames where that hydrogen bond is present. You can tell which series

column belongs to which hydrogen bond by the column header.

3) Calculate the standard deviation via the 'avg' analysis command.

For example:

# Phase 1: Calculate hydrogen bond series data

parm DPDP.parm7

trajin DPDP.nc

# Calculate backbone hydrogen bonds for certain residues.

# Solute-solute series data to uuseries.dat

# H. bond averages to avghb.dat

hbond BB :2-6,9-13.N,H,C,O series uuseries uuseries.dat avgout avghb.dat

# Phase 2: Calculate stdev for hydrogen bond of interest

# Read h. bond time series data.

readdata uuseries.dat name UU

parm DPDP.parm7

trajin DPDP.nc

# Filter out frames where h. bond corresponding to column 2 in uuseries.dat

# (in this case :13.O to :2.N-H) is not present.

filter UU:2 min 0.5 max 1.5

# Keep only those atoms involved in that h. bond.

strip !(:13.O|:2.N)

# Save those coordinates

createcrd H1

run

# Calculate the distance for the saved atoms.

crdaction H1 distance D1 @1 @2

# Get the average and standard deviation

runanalysis avg D1 out avg.dat name Avg

Note: There may be an easier way to do this with pytraj.

-Dan

On Tue, Jun 20, 2017 at 10:14 PM, Jag Silwal <jagsilwal.gmail.com> wrote:

*> Dear all,
*

*>
*

*> I did the h-bond analysis using cpptraj and I got following results in
*

*> "hbavg.dat". What I am looking for is the error (standard deviation)
*

*> associated with this average distance. For eg. For the following
*

*> 2.8751 ± ???
*

*>
*

*> I tried to look all the files from hydrogen bond analysis but I could
*

*> locate this information anywhere. Could someone please direct me on this?
*

*> DO I need to use specific instruction in cpptraj to get this separately?
*

*>
*

*> I would really appreciate your help.
*

*>
*

*> #Acceptor DonorH
*

*> Donor Frames Frac AvgDist
*

*> TYR_103.O_1631 ILE_18.H_258 ILE_18.N_257 8934
*

*> 0.9927 2.8751
*

*>
*

*> Sincerely,
*

*> Jag
*

*> Graduate Student
*

*> Michigan State Uiversity
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

Date: Wed, 21 Jun 2017 09:23:31 -0400

Hi,

The standard deviation for hydrogen bond distance and angle are not

currently tracked. It has been requested enough times that I'll

probably implement it at some point. I've added it to my 'hbond' to-do

list here: https://github.com/Amber-MD/cpptraj/issues/392

You can get this information with cpptraj as it is now but it takes a

few steps. You have to:

1) Make sure you record the time series data for hydrogen bonds

('series' keyword) and write it to a file ('uuseries' or 'uvseries').

2) In a separate run, use that data along with the 'filter' command to

save the atoms you will use to calculate the distance only for the

frames where that hydrogen bond is present. You can tell which series

column belongs to which hydrogen bond by the column header.

3) Calculate the standard deviation via the 'avg' analysis command.

For example:

# Phase 1: Calculate hydrogen bond series data

parm DPDP.parm7

trajin DPDP.nc

# Calculate backbone hydrogen bonds for certain residues.

# Solute-solute series data to uuseries.dat

# H. bond averages to avghb.dat

hbond BB :2-6,9-13.N,H,C,O series uuseries uuseries.dat avgout avghb.dat

# Phase 2: Calculate stdev for hydrogen bond of interest

# Read h. bond time series data.

readdata uuseries.dat name UU

parm DPDP.parm7

trajin DPDP.nc

# Filter out frames where h. bond corresponding to column 2 in uuseries.dat

# (in this case :13.O to :2.N-H) is not present.

filter UU:2 min 0.5 max 1.5

# Keep only those atoms involved in that h. bond.

strip !(:13.O|:2.N)

# Save those coordinates

createcrd H1

run

# Calculate the distance for the saved atoms.

crdaction H1 distance D1 @1 @2

# Get the average and standard deviation

runanalysis avg D1 out avg.dat name Avg

Note: There may be an easier way to do this with pytraj.

-Dan

On Tue, Jun 20, 2017 at 10:14 PM, Jag Silwal <jagsilwal.gmail.com> wrote:

-- ------------------------- 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jun 21 2017 - 06:30:05 PDT

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