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From: Duggan, Brendan M. <bmduggan.musc.edu>

Date: Mon, 20 Jul 2009 15:29:46 +0100

Hi Raja

I'm ccing this back to the Amber mailing list in the hope that someone there can give you additional information.

________________________________________

From: Raja Pandian [chemistryraj.gmail.com]

Sent: Saturday, July 18, 2009 7:43 AM

To: Duggan, Brendan M.

Subject: DCCM

Respected Duggan Brendan M,

Thanks for your suggestions!

I would like to do the Dynamic Cross Correlation Map (DCCM) analysis. Searching AMBER archive showed that similar questions have been posted before but no answer.

I have a question about the cross-correlation matrix calculation using ptraj (Amber 9). I use the following input for ptraj:

matrix correl name A_corr .CA out A_corr.dat

Using this ptraj command I got the Matrix (Diagonal Matrix) of the system.

Such as like, 5x5 matrix

1 2 3 4 5

2 1 6 7 8

3 6 1 8 9

4 7 8 1 2

5 8 9 2 1

One half is equal to another half…

How to generate the dynamic cross correlation matrix map using Cij=<∆ri*∆rj>/(<∆ri>2<∆rj>2)1/2 DCCM equation?

##

I'm not sure what equation ptraj uses. It doesn't seem to be documented in the manual so you would need to look in the source code. While you're looking at the source code it should not be too difficult to modify it to use the equation you want to use. Alternatively, you could use ptraj to generate a distance matrix then use a spreadsheet or some other mathematical or statistical package to do the calculations you want.

##

I have the three system (like A,B,and C), which contains the same amino acid sequence and those are differ only on metal site.

For this kind of system,

How to do DCCM analysis?

Whether it must be with in the system or between two systems? How to proceeds that one?

##

If I understand you correctly you have three different simulations of three slightly different systems, the difference being only in the metal binding site. In this case I believe you would have to do the correlation analysis of each simulation independently, then compare the results of each of those analyses.

##

Does the "correl" result give me the so-called "DCCM"? I noticed some publications showed the across-correlation map that was obtained form ptraj, it seems to me they never use the term DCCM.

##

Like I said in my previous reply, I believe the ptraj correl analysis is the same as DCCM. I had not seen the term DCCM before you posted it to the Amber mailing list but I believe its just a different name for the same thing.

##

How can I plot the correlation matrix map (A_corr.dat)? Could you please suggest me a graphic program for the correlation matrix data plot?

##

You could try either of the two I mentioned in my previous reply (Gnuplot, Bio3D package for R) or try any scientific graphing program like Mathematica or Origin

brendan

##

Thanks in advance for your suggestions.

Eagerly waiting for your reply!

Faithfully

Rajapandian. V

email: bmduggan.musc.edu

phone: (843) 792 5029

fax: (843) 792 4322

Received on Mon Jul 20 2009 - 10:09:34 PDT

Date: Mon, 20 Jul 2009 15:29:46 +0100

Hi Raja

I'm ccing this back to the Amber mailing list in the hope that someone there can give you additional information.

________________________________________

From: Raja Pandian [chemistryraj.gmail.com]

Sent: Saturday, July 18, 2009 7:43 AM

To: Duggan, Brendan M.

Subject: DCCM

Respected Duggan Brendan M,

Thanks for your suggestions!

I would like to do the Dynamic Cross Correlation Map (DCCM) analysis. Searching AMBER archive showed that similar questions have been posted before but no answer.

I have a question about the cross-correlation matrix calculation using ptraj (Amber 9). I use the following input for ptraj:

matrix correl name A_corr .CA out A_corr.dat

Using this ptraj command I got the Matrix (Diagonal Matrix) of the system.

Such as like, 5x5 matrix

1 2 3 4 5

2 1 6 7 8

3 6 1 8 9

4 7 8 1 2

5 8 9 2 1

One half is equal to another half…

How to generate the dynamic cross correlation matrix map using Cij=<∆ri*∆rj>/(<∆ri>2<∆rj>2)1/2 DCCM equation?

##

I'm not sure what equation ptraj uses. It doesn't seem to be documented in the manual so you would need to look in the source code. While you're looking at the source code it should not be too difficult to modify it to use the equation you want to use. Alternatively, you could use ptraj to generate a distance matrix then use a spreadsheet or some other mathematical or statistical package to do the calculations you want.

##

I have the three system (like A,B,and C), which contains the same amino acid sequence and those are differ only on metal site.

For this kind of system,

How to do DCCM analysis?

Whether it must be with in the system or between two systems? How to proceeds that one?

##

If I understand you correctly you have three different simulations of three slightly different systems, the difference being only in the metal binding site. In this case I believe you would have to do the correlation analysis of each simulation independently, then compare the results of each of those analyses.

##

Does the "correl" result give me the so-called "DCCM"? I noticed some publications showed the across-correlation map that was obtained form ptraj, it seems to me they never use the term DCCM.

##

Like I said in my previous reply, I believe the ptraj correl analysis is the same as DCCM. I had not seen the term DCCM before you posted it to the Amber mailing list but I believe its just a different name for the same thing.

##

How can I plot the correlation matrix map (A_corr.dat)? Could you please suggest me a graphic program for the correlation matrix data plot?

##

You could try either of the two I mentioned in my previous reply (Gnuplot, Bio3D package for R) or try any scientific graphing program like Mathematica or Origin

brendan

##

Thanks in advance for your suggestions.

Eagerly waiting for your reply!

Faithfully

Rajapandian. V

email: bmduggan.musc.edu

phone: (843) 792 5029

fax: (843) 792 4322

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