[gmx-users] regarding rmsd calculation of protein
SHAHEE ISLAM
islamshahee at gmail.com
Thu May 24 07:30:05 CEST 2018
after giving this command
make_ndx -f em.gro -o index.ndx
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
these all options are shown on the screen.
but when i am giving
> |
Syntax error: "|"
can you please tell me what should i give.
On 5/24/18, Soham Sarkar <soham9038 at gmail.com> wrote:
> It is any .gro file of your system
> You can make index file after final md
>
> On Thu, 24 May 2018, 10:37 am SHAHEE ISLAM, <islamshahee at gmail.com> wrote:
>
>> you have mention here em.gro,i think it is a gro file of
>> equilibration.can i make the index file after production run to
>> calculate rmsd.
>>
>> On 5/23/18, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
>> > thank you so much for your quick reply.
>> >
>> > On 5/23/18, Soham Sarkar <soham9038 at gmail.com> wrote:
>> >> Do proper indexing of each chain
>> >>> make_ndx -f em.gro -o index.ndx
>> >>>l (shows total residue with number)
>> >>>ri ( give numbers for residue number of each chain)
>> >>>rename them as Chain_A and Chain_B
>> >>>v (shows the newly indexed file)
>> >>>q (save)
>> >> Now your index has two chain seperated
>> >>
>> >> On Wed, May 23, 2018 at 5:54 PM, SHAHEE ISLAM <islamshahee at gmail.com>
>> >> wrote:
>> >>
>> >>> hi,
>> >>> i have two protein in my gro file.when i am calculating rmsd by this
>> >>> command
>> >>> g_rms -s dynamic.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
>> >>> this options are coming
>> >>> Group 0 ( System) has 12059 elements
>> >>> Group 1 ( Protein) has 566 elements
>> >>> Group 2 ( Protein-H) has 566 elements
>> >>> Group 3 ( C-alpha) has 0 elements
>> >>> Group 4 ( Backbone) has 0 elements
>> >>> Group 5 ( MainChain) has 0 elements
>> >>> Group 6 ( MainChain+Cb) has 0 elements
>> >>> Group 7 ( MainChain+H) has 0 elements
>> >>> Group 8 ( SideChain) has 566 elements
>> >>> Group 9 ( SideChain-H) has 566 elements
>> >>> Group 10 ( Prot-Masses) has 566 elements
>> >>> Group 11 ( non-Protein) has 11493 elements
>> >>> Group 12 ( Other) has 11493 elements
>> >>> Group 13 ( W) has 11477 elements
>> >>> Group 14 ( ION) has 16 elements
>> >>> for this reason i am able to calculate the rmsd of two protein
>> >>> together by selecting 1.
>> >>> but i want to calculate the rmsd of the protein individualy.how i
>> >>> will
>> >>> do
>> >>> this.
>> >>> My .gro file consist of atom no 1 to 283 for protein1 and atom no 284
>> >>> to 566 for protein2.
>> >>> thanking you
>> >>> shahee islam
>> >>> university of calcutta
>> >>> --
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>> >>
>> >>
>> >>
>> >> --
>> >> SOHAM SARKAR
>> >> Junior Research Fellow
>> >> Department of Chemistry
>> >> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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