these are in continuity I mean for the ffbonded.itp file<br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G <span dir="ltr"><<a href="mailto:gtrama@gmail.com">gtrama@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">more parameters - ffbonded.itp<br>NB CT 1 0.1444 294553.6<br>NB C 1 0.1404 334720.0<br>
C CC 1 0.1407 343088.0<br>CC CB 1 0.1474 468608.0<br> CB H2 1 0.1076 129960.25<br>
<br>to aminoacids.hdb<br>1 1 HE2 CE2 CZ CD2<br>1 1 HE1 CE1 CZ CD1<br>1 1 HD1 CD1 CG2 CE1<br>1 1 HD2 CD2 CG2 CE2<br>1 2 HH OH CZ CE1<br>
1 1 HB2 CB2 CA2 CG2<br>1 2 HG1 OG1 CB1 CA1<br>1 1 H N CA1 C1<div><div></div><div class="h5"><br><br><br><br><br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 12:18 AM, Ramachandran G <span dir="ltr"><<a href="mailto:gtrama@gmail.com" target="_blank">gtrama@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">For ffbonded.itp, i added the following. (you need to be carefull here since i cooked upto the force constants)<br>
C CC CB CA 9 180.0 4.309 1<br> NB CC C O 9 180.0 4.309 1 ;<br> NB CC CB CA 9 180.0 4.309 1<br>
NB CC CB H2 9 180.0 4.309 1<br> C CC CB H2 9 180.0 4.309 1<br> NB CC C NB 9 180.0 4.0876 1<br> CT NB C CC 9 180.0 4.0876 1<br> CT NB C O 9 180.0 4.0876 1<br>
CB CC C NB 9 180.0 4.0876 1<br> CB CC C O 9 180.0 4.0876 1<br> CC C NB CC 9 180.0 4.7656 1<br> O C NB CC 9 180.0 4.7656 1;<br> CC NB CT C 9 180.0 4.1400 1;<br>
C NB CT C 9 180.0 4.1400 1 ;<br> CT CT OH HO 4 180.0 4.1400 1 ; <br> OH CT CT CC 9 0.0 4.1400 1<br> OH CT CT N 9 180.0 4.9162 1<br><br>; added newly improper dihedrals<br>
CB CC CA H2 4 180.0 4.1840 2<br> CC NB CB C 4 180.0 4.1840 2<br> CC CT NB NB 4 180.0 4.1840 2<br> CT N CC CT 4 144.64 3.1840 2<br> NB O CC C 4 180.0 4.1840 2<br>
NB CC C CT 4 180.0 4.1840 2<br> CA CB CA CA 4 180.0 4.1840 2<br> CA HA CA CA 4 180.0 4.1840 2<br>; added to test<br> N CT C H 4 180.0 4.1840 2<div>
<div></div><div><br>
<br><br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 12:13 AM, Ramachandran G <span dir="ltr"><<a href="mailto:gtrama@gmail.com" target="_blank">gtrama@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
For the GFP chromophore i name residue as CRIH.<br>1. aminoacids.rtp<br> CB2 CB 0.019103 1<br> CA2 CC -0.026635 2<br> N2 NB -0.436463 3<br> C1 CC 0.302706 4<br>
N3 NB -0.541478 5<br> C2 C 0.563844 6<br> OC2 O -0.394118 7<br> CG2 CA -0.079330 8<br> CZ CA 0.240178 9<br> CD1 CA -0.072596 10<br>
HD1 HA 0.129374 11<br> CD2 CA -0.070677 12<br> HD2 HA 0.091532 13<br> CE1 CA -0.129374 14<br> HE1 HA 0.091792 15<br> CE2 CA -0.087778 16<br>
HE2 HA 0.112301 17<br> OH OH -0.454413 18<br> H H 0.37107 19<br> HH HO 0.258435 20<br> N N -0.61682 21<br> CA1 CT -0.116631 22<br>
CB1 CT -0.03127 23<br> OG1 OH -0.74662 24<br> HG1 HO 0.45887 25<br> HB2 H2 0.116716 26<br> CA3 CT -0.250251 27<br> C C 0.35254 28<br>
O O -0.48366 29<br> [ bonds ]<br> C1 CA1<br> N3 CA3<br> N3 C1<br> N3 C2<br> C2 OC2<br> C1 N2<br> C2 CA2<br> N2 CA2<br>
CA2 CB2<br> CB2 CG2<br> CG2 CD1<br> CG2 CD2<br> CD1 CE1<br> CD2 CE2<br> CE1 CZ<br> CE2 CZ<br> CZ OH<br> CB1 OG1<br> OH HH<br>
CB2 HB2<br> CD1 HD1<br> CD2 HD2<br> CE1 HE1<br> CE2 HE2<br> CA1 N<br> CA1 CB1<br> CA3 C<br> C O<br> OG1 CB1<br> OG1 HG1<br>
N H<br> -C N<br> +N C<br> [ angles ]<br> ; ai aj ak th0 cth ub0 cub<br> N2 C1 N3 114.0 1087.87<br> C1 N2 CA2 106.0 1087.87<br>
C1 N3 C2 107.9 1087.87<br> N2 CA2 C2 108.3 1087.87<br> N2 CA2 CB2 129.5 376.56<br> C2 N3 CA3 123.4 267.776<br> N3 C2 OC2 126.0 351.456<br>
N3 C2 CA2 103.0 1087.87<br> OC2 C2 CA2 132.0 317.984<br> C2 CA2 CB2 122.0 376.56<br> CA2 CB2 CG2 130.0 1087.87<br> CB2 CG2 CD1 121.0 383.2544<br>
CB2 CG2 CD2 121.0 383.2544<br> CG2 CD1 CE1 120.0 334.72<br> CG2 CD2 CE2 120.0 334.72<br> CD1 CG2 CD2 120.0 334.72<br> CD1 CE1 CZ 120.0 334.72<br>
CD2 CE2 CZ 120.0 334.72<br> CE1 CZ CE2 120.0 334.72<br> OH CZ CE1 120.0 378.2336<br> OH CZ CE2 120.0 378.2336<br> HH OH CZ 108.0 543.92<br>
HG1 OG1 CB1 108.0 543.92<br> N2 C1 CA1 125.0 334.72<br> N3 C1 CA1 121.4 292.88<br> C1 N3 CA3 129.0 301.248<br> HB2 CB2 CA2 114.0 351.456<br>
HB2 CB2 CG2 116.0 351.456<br> HD1 CD1 CG2 120.0 251.04<br> HD1 CD1 CE1 120.0 251.04<br> HD2 CD2 CG2 120.0 251.04<br> HD2 CD2 CE2 120.0 251.04<br>
HE1 CE1 CZ 120.0 251.04<br> HE1 CE1 CD1 120.0 251.04<br> HE2 CE2 CZ 120.0 251.04<br> HE2 CE2 CD2 120.0 251.04<br> CA1 N H 118.4 317.984<br>
CA1 CB1 OG1 109.5 669.44<br> N CA1 CB1 109.7 669.44<br> CB1 CA1 C1 111.1 527.184<br> CA3 C O 120.4 669.44<br> N CA1 C1 110.1 527.184<br>
C CA3 N3 110.3 669.44<br> CA3 C N 116.6 585.76<br> C2 CA2 CB2 CG2 ;<br> N2 CA2 CB2 CG2<br> CA2 CB2 CG2 CD1 ;<br> CA2 CB2 CG2 CD2 ;<br>
N2 CA2 CB2 HB2<br> C2 CA2 CB2 HB2<br> HB2 CB2 CG2 CD1 ;<br> HB2 CB2 CG2 CD2 ;<br> CB2 CG2 CD1 CE1 ;<br> CB2 CG2 CD2 CE2 ;<br> CD1 CE1 CZ CE2<br>
CD1 CE1 CZ OH<br> CE1 CZ OH HH<br> CE2 CZ OH HH<br> CG2 CD1 CE1 CZ<br> HD1 CD1 CG2 CD2<br> HD1 CD1 CE1 CZ<br> HD2 CD2 CG2 CD1<br>
HD2 CD2 CE2 CZ<br> HE1 CE1 CD1 CG2<br> HE1 CE1 CZ CE2<br> HE2 CE2 CD2 CG2<br> HE2 CE2 CZ CE1<br> CA1 C1 N2 CA2 ;<br> CA1 C1 N3 C2 ;<br>
CA3 N3 C2 CA2<br> CA3 N3 C1 N2 ;<br> CG2 CB2 CA2 N2 ; repeated<br> CG2 CB2 CA2 C2 ; repeated<br> CB2 CA2 N2 C1<br> CB2 CA2 C2 N3<br>
CA2 N2 C1 N3<br> CA2 C2 N3 C1<br> OG1 CB1 CA1 C1 ;<br> OG1 CB1 CA1 N ;<br> CA1 CB1 OG1 HG1 ;<br> N3 CA3 C O ;<br> OC2 C2 CA2 CB2 ; <br>
OC2 C2 N3 CA3 ; <br> OC2 C2 CA2 N2 ; <br> OC2 C2 N3 C1 ; <br> N3 CA3 C +N ; added to link the neighbouring valine<br> CA3 C +N +H ; <br>
CA3 C +N +CA ; <br> CB1 CA1 N -C ; added to link the neighbouring PHE<br> C1 CA1 N -C ; <br> CA1 N -C -O ; <br> H N -C -O ; n<br>
[ impropers ]<br> C1 CA1 N2 N3<br> CA2 N2 CB2 C2<br> C2 CA2 OC2 N3<br> CG2 CB2 CD1 CD2<br> CZ CE1 CE2 OH<br> N3 C1 C2 CA3<br>
CB2 CA2 CG2 HB2<br> CD1 CG2 HD1 CE1<br> CD2 CG2 HD2 CE2<br> CE1 CD1 HE1 CZ<br> CE2 CD2 HE2 CZ<br> CA1 N C1 CB1<br>
C CA3 N O ;<br> N CA1 C H ;<br><br><br><br><br><br>
</blockquote></div><br><br clear="all"><br></div></div><div><div></div><div>-- <br>Postdoctoral Research Scholar,<br>Department of Chemistry,<br>University of Nevada, Reno.<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Postdoctoral Research Scholar,<br>Department of Chemistry,<br>University of Nevada, Reno.<br>
</div></div><br>--<br>
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