Dear all
Sorry for bothering you with such a silly problem. I found a solution
myself. I specified the output as a .xls file and used Libre Office to open
it in a spreadsheet. I used separator option as space and merged
delimiters. Now I get an absolutely fine 120x120 matrix!
Cheers
Suchetana
On Wed, Jan 21, 2015 at 9:31 AM, Suchetana Gupta <bt13d072.smail.iitm.ac.in>
wrote:
> Hi Dan
> Thanks for the suggestions. I tried using small residue selections and
> they are working fine in Amber12. But the moment I increase the number of
> residues, the output file doesn't contain the data in the correct matrix
> format. I am sure I am getting 120x120 values, but the output is not in a
> matrix format. I am attaching a screenshot if it helps.
> Any help would be appreciated.
> Thanks
>
> On Tue, Jan 20, 2015 at 11:49 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>> Hi,
>>
>> On Tue, Jan 20, 2015 at 6:40 AM, Suchetana Gupta bt13d072
>> <bt13d072.smail.iitm.ac.in> wrote:
>> > trajin last_20_stripped_imaged.cdf
>> > rms first mass :1-120
>> > matrix correl :1-120.CA out last_20_wt_correl.txt byres
>> >
>> > However, the output matrix file is not in a 120 X 120 format. Instead, I
>> > see data in a random fashion. So much so, that I am unable to understand
>> > which value corresponds to which residue. Is there any method to get the
>> > output in a 120X120 matrix?
>>
>> It's not clear what you mean by "random fashion". Have you run the
>> tests for your Amber installation? You should absolutely get a file
>> containing 120 rows and 120 columns. Try it on a smaller number of
>> residues first to become familiar with the output. For example, a 4
>> residue selection (:1-4) will give output containing 4 rows and 4
>> columns like so:
>>
>> 1.00 0.38 0.23 0.02
>> 0.38 1.00 0.46 -0.40
>> 0.23 0.46 1.00 0.24
>> 0.02 -0.40 0.24 1.00
>>
>> The first row and column is residue 1 to 1, the first row and second
>> column is residue 1 to 2, etc. Hope this helps,
>>
>> -Dan
>>
>> PS - Also, consider upgrading to AmberTools 14 (which is free), as it
>> contains more functionality and bug fixes. Also consider using cpptraj
>> instead (ptraj is no longer being actively developed).
>>
>> >
>> > Thanks in advance for your help
>> > Suchetana Gupta
>> > IIT Madras
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Jan 20 2015 - 21:00:02 PST
