<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 11/06/2012 6:12 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzQOiy0spdWZhA6DdqE0NC-SZr8kRV7qRHYgcQYuzaCtg@mail.gmail.com"
type="cite">Justin<br>
<br>
<br>
1) So if I understood correctly I can make parametrisation of my
uncommon group by the atb for instance. Than I can change itp file
to rtp form and integrate this new residue to the existing ff.
Finally when I will run pdb2gmx on the protein with the same group
(even with different atom order) I obtain proper topology.top
file. Doest it correct ?<br>
</blockquote>
<br>
The "change" to which you refer will be non-trivial because of the
covalent bond. Charge distribution and atom types will change.<br>
<br>
<blockquote
cite="mid:CAALQopzQOiy0spdWZhA6DdqE0NC-SZr8kRV7qRHYgcQYuzaCtg@mail.gmail.com"
type="cite"><br>
2) I've defined bond between both of my atoms as the gb_15 and
define this atoms as the C in the topology.top. Than I've run
minimisation and short 3ns MD_run. Unfortunatelly this atoms was
in the sp3 form and were not in the planar form :( What else
should I do ? Could some operations with the angle term in
topology.top help me? I've modified 612 613 614 2 as the
ga_27 but it also could not help me.<br>
</blockquote>
<br>
It is possible to hack something that will work, but the
transferability of charges from an isolated form to a form
covalently bound to a peptide is (at best) doubtful. If your atomic
arrangement is changing, the presence of single vs double bonds must
be changing, and that should basically guarantee
non-transferability.<br>
<br>
The most correct form of a solution is to parameterise the modified
form of the residue along the same lines as the original force field
parameterization. That may or may not be feasible for you. It's hard
to be more specific without knowing exactly what modified residue
you are seeking to create. <br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzQOiy0spdWZhA6DdqE0NC-SZr8kRV7qRHYgcQYuzaCtg@mail.gmail.com"
type="cite">
<br>
<br>
<br>
James<br>
<br>
<div class="gmail_quote">2012/6/10 Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On 6/10/12 8:03 AM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<br>
thanks again for help.<br>
<br>
Finally is there any generall solution to parametrise
hetero-groups covalently<br>
bonded with the protein ? Many proteins consist of such
groups e.g chromophore<br>
in GFP, retinall in rhodopsin as well as some prostetic
groups in the enzymes.<br>
<br>
</blockquote>
<br>
</div>
Parameterization schemes differ across force fields. It's
never easy.
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
I've tried to make something like you've told me via
inclusion of<br>
pre-parametrised residues in the existing gromacs ff but
forced with some<br>
problems due to the atom order in new ITP and gro files
provided by ATb or<br>
PRODRG are different from initial pdb file so pdb2gmx on
the whole protein where<br>
het-group in the old order would not work properly :(<br>
<br>
</blockquote>
<br>
</div>
The output .itp files of ATB or PRODRG are not what you should
be using. You can't #include a covalently attached residue
and expect the resulting dynamics to be relevant; it's not
like a ligand.<br>
<br>
What you need to do in those cases is create an .rtp entry
(and any other incidental bonded and nonbonded additions, as
stated before) that specifies whatever parameters you believe
to be reliable. At that point, when the .rtp file is read,
the atom order is irrelevant - if pdb2gmx finds the atoms it
needs, it builds the topology.
<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div>
</div>
</blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>