<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 4/02/2011 12:36 PM, william Stebbeds wrote:
<blockquote cite="mid:BLU118-W2432850A6376CDE80EC389C1E60@phx.gbl"
type="cite">
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
Thanks for the reply,<br>
<br>
ffamber99sb.rtp entry:<br>
[ DGO ]<br>
[ atoms ]<br>
P amber99_46 1.16590 1<br>
O1P amber99_45 -0.77610 2<br>
O2P amber99_45 -0.77610 3<br>
O5' amber99_44 -0.49540 4<br>
C5' amber99_11 -0.00690 5<br>
H5'1 amber99_19 0.07540 6<br>
H5'2 amber99_19 0.07540 7<br>
C4' amber99_11 0.16290 8<br>
H4' amber99_19 0.11760 9<br>
O4' amber99_44 -0.36910 10<br>
C1' amber99_11 0.03580 11<br>
H1' amber99_20 0.17460 12<br>
N9 amber99_40 0.05770 13<br>
C8 amber99_6 0.07360 14<br>
O8 amber99_44 -0.36910 15<br>
N7 amber99_36 -0.57250 16<br>
C5 amber99_4 0.19910 17<br>
C6 amber99_2 0.49180 18<br>
O6 amber99_41 -0.56990 19<br>
N1 amber99_35 -0.50530 20<br>
H1 amber99_17 0.35200 21<br>
C2 amber99_3 0.74320 22<br>
N2 amber99_38 -0.92300 23<br>
H21 amber99_17 0.42350 24<br>
H22 amber99_17 0.42350 25<br>
N3 amber99_37 -0.66360 26<br>
C4 amber99_4 0.18140 27<br>
C3' amber99_11 0.07130 28<br>
H3' amber99_19 0.09850 29<br>
C2' amber99_11 -0.08540 30<br>
H2'1 amber99_18 0.07180 31<br>
H2'2 amber99_18 0.07180 32<br>
O3' amber99_44 -0.52320 33<br>
[ bonds ]<br>
P O1P<br>
P O2P<br>
P O5'<br>
O5' C5'<br>
C5' H5'1<br>
C5' H5'2<br>
C5' C4'<br>
C4' H4'<br>
C4' O4'<br>
C4' C3'<br>
O4' C1'<br>
C1' H1'<br>
C1' N9<br>
C1' C2'<br>
N9 C8<br>
N9 C4<br>
C8 O8<br>
C8 N7<br>
N7 C5<br>
C5 C6<br>
C5 C4<br>
C6 O6<br>
C6 N1<br>
N1 H1<br>
N1 C2<br>
C2 N2<br>
C2 N3<br>
N2 H21<br>
N2 H22<br>
N3 C4<br>
C3' H3'<br>
C3' C2'<br>
C3' O3'<br>
C2' H2'1<br>
C2' H2'2<br>
-O3' P<br>
[ dihedrals ]<br>
O4' C1' N9 C4 proper_X_CT_N*_X <br>
C1' N9 C8 O8 proper_X_CK_N*_X<br>
C1' N9 C8 N7 proper_X_CK_N*_X<br>
C1' N9 C4 C5 proper_X_CB_N*_X<br>
C1' N9 C4 N3 proper_X_CB_N*_X<br>
H1' C1' N9 C8 proper_X_CT_N*_X <br>
H1' C1' N9 C4 proper_X_CT_N*_X <br>
C8 N9 C4 C5 proper_X_CB_N*_X<br>
C8 N9 C4 N3 proper_X_CB_N*_X<br>
C5 C6 N1 H1 proper_X_C_NA_X<br>
C5 C6 N1 C2 proper_X_C_NA_X<br>
C6 N1 C2 N2 proper_X_CA_NA_X<br>
C6 N1 C2 N3 proper_X_CA_NA_X<br>
O6 C6 N1 H1 proper_X_C_NA_X<br>
O6 C6 N1 C2 proper_X_C_NA_X<br>
N1 C2 N3 C4 proper_X_CA_NC_X<br>
H1 N1 C2 N2 proper_X_CA_NA_X<br>
H1 N1 C2 N3 proper_X_CA_NA_X<br>
N2 C2 N3 C4 proper_X_CA_NC_X<br>
H8 C8 N7 C5 proper_X_CK_NB_X<br>
N9 C8 N7 C5 proper_X_CK_NB_X<br>
H8 C8 N9 C4 proper_X_CK_N*_X<br>
N7 C8 N9 C4 proper_X_CK_N*_X<br>
O4' C1' C2' H2'1 proper_H_CT_CT_O<br>
O4' C1' C2' H2'2 proper_H_CT_CT_O<br>
O3' C3' C2' H2'1 proper_H_CT_CT_O<br>
O3' C3' C2' H2'2 proper_H_CT_CT_O<br>
[ impropers ]<br>
C4 C8 N9 C1' nucleic_imp_10<br>
C5 N1 C6 O6<br>
C6 C2 N1 H1 nucleic_imp_10<br>
C2 H21 N2 H22<br>
N9 N7 C8 O8<br>
N2 N1 C2 N3 nucleic_imp_11<br>
<br>
DGO was also added to residuetypes.dat. hdb file was also updated,
as was dna.rtp within amber99sb.ff.<br>
<br>
The problem is not a simple missing bond, as when the structure
goes through pdb2gmx, the new nucleotide appears on the other side
of the pbc, in a straight line (i.e. without form).<br>
</blockquote>
<br>
Are you saying the coordinate file you gave to pdb2gmx has your
modified residue at one location, and the coordinate file it output
has it at some other location? (Because I doubt it). Please show us
the sections of those coordinate files including your modified
residue and a few atoms either side.<br>
<br>
Also, what is your pdb2gmx command line and for what GROMACS
version?<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:BLU118-W2432850A6376CDE80EC389C1E60@phx.gbl"
type="cite"><br>
Thanks<br>
<br>
Will<br>
<br>
> Date: Thu, 3 Feb 2011 16:07:42 -0500<br>
> From: <a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: Re: [gmx-users] Adding modified nucleotide to a
forcefield<br>
> <br>
> <br>
> <br>
> william Stebbeds wrote:<br>
> > Hello,<br>
> > <br>
> > I am attempting to add 8-oxo-dG
(8-Oxo-2'-deoxyguanosine) to the <br>
> > amber99sb force field. This is a simple modification of
the H8 hydrogen <br>
> > on a guanine to an oxygen atom. I have followed the
instructions on the <br>
> > gromacs site on adding residues.<br>
> > <br>
> > However the new nucleotide will not work, it will not
attach to the <br>
> > adjacent nucleotides in the sequence.<br>
> > <br>
> <br>
> So a bond is missing?<br>
> <br>
> > Any help would be very much appreciated, if any more
information is <br>
> > required please let me know.<br>
> > <br>
> <br>
> A lot more information is needed, at the very least, your
.rtp entry.<br>
> <br>
> -Justin<br>
> <br>
> > Best Regards<br>
> > <br>
> > William Stebbeds<br>
> > Cranfield University<br>
> > UK<br>
> > <br>
> <br>
> -- <br>
> ========================================<br>
> <br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]vt.edu | (540) 231-9080<br>
> <a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
> <br>
> ========================================<br>
> -- <br>
> gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before
posting!<br>
> Please don't post (un)subscribe requests to the list. Use the
<br>
> www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
<br>
</body>
</html>