bharat gupta wrote:
On Fri, Jan 21, 2011 at 3:32 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
bharat gupta wrote:
I want to calculate the rmsd of amino acid 65 to 67 of two
simulated proteins with loop replacement in another one to find
out how the position of these 3 amino acids change due to the
replacement of a loop region in same protein ... How can I
achieve it with gromacs...
Use g_rms with a suitable index group.
-Justin
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com <mailto:monu46...@yahoo.com>>
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com <mailto:monu46...@yahoo.com>>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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I am not able to search some relevant document about creating index
group fro g_rms ... I found one i gromacs website
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive but
this link doesnot explain much about it ... can u pls guide me to some
relevant link ??
See the manual, section 8.1 and appendix D.83. If you search the Gromacs site
for "index group" you will find (among others):
http://www.gromacs.org/Documentation/File_Formats/Index_File
-Justin
I am stating my question here again : I want to calculate the rmsd of
amino acid 65 to 67 of two simulated proteins with loop replacement in
another one to find out how the position of these 3 amino acids change
due to the replacement of a loop region in same protein ... How can I
achieve it with gromacs...
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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