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<TD>Dear Sir,<BR><BR> As you told I first created an index file by using make_ndx command as<BR>follows ( here I selected group 1 and entered q to save and quit).<BR><BR><BR>There are: 3027 OTHER residues<BR><BR>There are: 1 PROTEIN residues<BR><BR>There are: 0 DNA residues<BR><BR>Analysing Protein...<BR><BR>Analysing Other...<BR><BR><BR>0 System : 9369 atoms<BR><BR>1 Protein : 288 atoms<BR><BR>2 Protein-H : 288 atoms<BR><BR>3 C-alpha : 0 atoms<BR><BR>4 Backbone : 0 atoms<BR><BR>5 MainChain : 0 atoms<BR><BR>6 MainChain+Cb : 0 atoms<BR><BR>7 MainChain+H : 0 atoms<BR><BR>8 SideChain : 288 atoms<BR><BR>9 SideChain-H : 288 atoms<BR><BR>10 Prot-Masses : 288 atoms<BR><BR>11 Non-Protein : 9081 atoms<BR><BR>12 SOL : 9081 atoms<BR><BR>13 Other : 9081 atoms<BR><BR><BR>nr : group ! =20<BR>'name' nr name 'splitch' nr 'l': list<BR>residues<BR><BR>'a': atom =20<BR>& 'del'<BR>nr 'splitres'<BR>nr 'h': help<BR><BR>'t': atom type | 'keep' nr 'splitat' nr<BR><BR>'r': residue =20<BR>'res': group res 'chain' char 'q': save and quit<BR><BR>"name": group 'case':<BR>case<BR>sensitive =20<BR>'v': verbose output<BR><BR><BR>> 'protein'<BR><BR><BR>Copied index group 1 'Protein'<BR><BR><BR>14 Protein : 288 atoms<BR><BR>> q<BR><BR><BR>Then I used g_mindist command to get the end-to-end distance of the polymer=<BR>chain as follows:<BR><BR><BR>You can compute the distances between a first group<BR><BR>and a number of other groups.<BR><BR>How many other groups do you want (>=3D 1) ?<BR><BR>1<BR><BR>Group 0 ( System) has 9369 elements<BR><BR>Group 1 ( Protein) has 288 elements<BR><BR>Group 2 ( Protein-H) has 288 elements<BR><BR>Group 3 ( C-alpha) has 0 elements<BR><BR>Group 4 ( Backbone) has 0 elements<BR><BR>Group 5 ( MainChain) has 0 elements<BR><BR>Group 6 (MainChain+Cb) has 0 elements<BR><BR>Group 7 ( MainChain+H) has 0 elements<BR><BR>Group 8 ( SideChain) has 288 elements<BR><BR>Group 9 ( SideChain-H) has 288 elements<BR><BR>Group 10 ( Prot-Masses) has 288 elements<BR><BR>Group 11 ( Non-Protein) has 9081 elements<BR><BR>Group 12 ( SOL) has 9081 elements<BR><BR>Group 13 ( Other) has 9081 elements<BR><BR>Group 14 ( Protein) has 288 elements<BR><BR>Select a group: 1<BR><BR>Selected 1: 'Protein'<BR><BR>Select a group: 1<BR><BR>Selected 1: 'Protein'<BR><BR>Reading frame 0 time 0.000<BR><BR>Back Off! I just backed up mindist.xvg to ./#mindist.xvg.1#<BR><BR>Last frame 1000 time 1000.000<BR><BR><BR>Is this correct or I am doing wrong? PLease help me out.<BR><BR>Thanking you in advance.<BR><BR><BR>Rahul Karyappa<BR><BR>NCL, Pune<BR><BR><BR><BR><BR><BR><BR><BR><BR>_______________________________________________<BR><BR><BR>------=_Part_1_4306485.1127105747375<BR>Content-Type: text/html<BR>Content-Transfer-Encoding: quoted-printable<BR><BR><HTML><HEAD><META content=3D"text/html; charset=3Dx-user-defined" http-equi=<BR>v=3D"Content-Type"><style type=3D"text/css"><!--.MailHeader { font-family: =<BR>"Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: n=<BR>ormal; text-decoration: none; }//--></style></HEAD><BODY><BR><br><font face=3D"Arial" size=3D"2"><TABLE STYLE=3D"border-color: blue; bor=<BR>der-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD>Dear Sir,<br><BR>I am mailing this second time. Please reply this mail. As you told I first =<BR>created index file by using make_ndx command as<BR>follows ( here I selected group 1 and entered q to save and quit).<br><BR><br><BR><font size=3D"2">There are: 3027 OTHER residues<br><BR>There are: 1 PROTEIN residues<br><BR>There are: 0 DNA residues<br><BR>Analysing Protein...<br><BR>Analysing Other...<br><BR><br><BR>0 System : 9369 atoms<br><BR>1 Protein : 288 atoms<br><BR>2 Protein-H : 288 atoms<br><BR>3 C-alpha : 0 atoms<br><BR>4 Backbone : 0 atoms<br><BR>5 MainChain : 0 atoms<br><BR>6 MainChain+Cb : 0 atoms<br><BR>7 MainChain+H : 0 atoms<br><BR>8 SideChain : 288 atoms<br><BR>9 SideChain-H : 288 atoms<br><BR>10 Prot-Masses : 288 atoms<br><BR>11 Non-Protein : 9081 atoms<br><BR>12 SOL : 9081 atoms<br><BR>13 Other : 9081 atoms<br><BR><br><BR>nr : group ! =20<BR>'name' nr name 'splitch' nr 'l': list<BR>residues<br><BR>'a': atom =20<BR>&amp; 'del'<BR>nr 'splitres'<BR>nr 'h': help<br><BR>'t': atom type | 'keep' nr 'splitat' nr<br><BR>'r': residue =20<BR>'res': group res 'chain' char 'q': save and quit<br><BR>"name": group 'case':<BR>case<BR>sensitive =20<BR>'v': verbose output<br><BR><br><BR>&gt; 'protein'<br><BR><br><BR>Copied index group 1 'Protein'<br><BR><br><BR>14 Protein : 288 atoms<br><BR>&gt; q<br><BR><br><BR><font size=3D"3">Then I used g_mindist command to get the end-to-end distan=<BR>ce of the polymer chain as follows:<br><BR><font size=3D"2"><br><BR>You can compute the distances between a first group<br><BR>and a number of other groups.<br><BR>How many other groups do you want (&gt;=3D 1) ?<br><BR>1<br><BR>Group 0 ( System) has 9369 elements<br><BR>Group 1 ( Protein) has 288 elements<br><BR>Group 2 ( Protein-H) has 288 elements<br><BR>Group 3 ( C-alpha) has 0 elements<br><BR>Group 4 ( Backbone) has 0 elements<br><BR>Group 5 ( MainChain) has 0 elements<br><BR>Group 6 (MainChain+Cb) has 0 elements<br><BR>Group 7 ( MainChain+H) has 0 elements<br><BR>Group 8 ( SideChain) has 288 elements<br><BR>Group 9 ( SideChain-H) has 288 elements<br><BR>Group 10 ( Prot-Masses) has 288 elements<br><BR>Group 11 ( Non-Protein) has 9081 elements<br><BR>Group 12 ( SOL) has 9081 elements<br><BR>Group 13 ( Other) has 9081 elements<br><BR>Group 14 ( Protein) has 288 elements<br><BR>Select a group: 1<br><BR>Selected 1: 'Protein'<br><BR>Select a group: 1<br><BR>Selected 1: 'Protein'<br><BR>Reading frame 0 time 0.000<br><BR>Back Off! I just backed up mindist.xvg to ./#mindist.xvg.1#<br><BR>Last frame 1000 time 1000.000</font><br><BR><br><BR>Is this correct or I am doing wrong? PLease help me out.<br><BR>Thanking you in advance.<br><BR><br><BR>Rahul Karyappa<br><BR>NCL, Pune<br><BR></font><br><BR><br><BR><br><BR><br><BR></font><font face=3D"Arial" size=3D"2"><TABLE STYLE=3D"border-color: blue; =<BR>border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><br><BR></TD></TR></tbody></TABLE></font><TABLE><tbody><TR><TD BGCOLOR=3D"#ffffff">=<BR><font color=3D"#000000"><BR></font><br><BR></TD></TR></tbody></TABLE>_______________________________________________<b=<BR>r><br><BR></TD></TR></tbody></TABLE></font></BODY></HTML><BR>------=_Part_1_4306485.1127105747375--<BR><BR><BR>*****************************************************************<BR>This email is virus free by TrendMicro Inter Scan Security Suite.<BR>*****************************************************************<BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. 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