<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-9"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 30/12/2010 11:37 PM, ahmet yıldırım wrote:
<blockquote
cite="mid:AANLkTimk1bvkfY5qpna3Vc6OcuJaPqoSfCPXtvVJaBVn@mail.gmail.com"
type="cite">Dear Justin,<br>
<br>
Firstly, Thanks for your help. You said "You're going from the end
of chain B to the beginning of chain A, then back to B later on.
Also realize that whatever "ABSG" or "BSG" is." <span
id="result_box" class="short_text" lang="en"><span
title="Alternatif çevirileri görmek için tıklayın" class="hps">How</span>
<span title="Alternatif çevirileri görmek için tıklayın"
class="hps">do you understand</span> <span title="Alternatif
çevirileri görmek için tıklayın" class="hps">it? </span></span><span
id="result_box" class="" lang="en"><span title="Alternatif
çevirileri görmek için tıklayın" class="hps">Where</span> <span
title="Alternatif çevirileri görmek için tıklayın" class="hps">can
I find</span> <span title="Alternatif çevirileri görmek için
tıklayın" class="hps">such</span> <span title="Alternatif
çevirileri görmek için tıklayın" class="hps">an important</span>
<span title="Alternatif çevirileri görmek için tıklayın"
class="hps">theoretical</span> <span title="Alternatif
çevirileri görmek için tıklayın" class="hps">information</span><span
class="" title="Alternatif çevirileri görmek için tıklayın">?</span></span><br>
</blockquote>
<br>
In order to understand the contents of a PDB file, you need to have
an understanding of its format. Unfortunately, it is a complex
format because PDB is used for many things. Several emails ago I
think I suggested that you should look for that format... hint,
hint. Perhaps the RCSB site also has a simpler introduction to the
topic, too.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimk1bvkfY5qpna3Vc6OcuJaPqoSfCPXtvVJaBVn@mail.gmail.com"
type="cite">
<br>
Thanks in advance<br>
<br>
<div class="gmail_quote">29 Aralık 2010 20:07 tarihinde Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
OK. if I do what sort change in pdb file, there is no need
to create .rtp file. It seems difficult to create the .rtp
file.<br>
<br>
</blockquote>
<br>
</div>
That depends on whether you need this residue, hence all of my
previous questions. If there is some functional significance
to this residue and you need it for a simulation, then you'll
either need to deal with the .rtp file, which actually is not
terribly difficult, it just involves a little bit of reading
and studying existing examples. Otherwise, if the molecule is
non-covalently bound to the protein, follow the tutorial I
linked before, and pay attention to the hint I gave you before
about using PRODRG, which I will reiterate more explicitly:
the output topology from PRODRG will require manual
modification and validation.<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips"
target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Thanks for your help<br>
<br>
29 Aralık 2010 19:49 tarihinde Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a> <mailto:<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>>> yazdı:
<div class="im">
<br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
You said "You do not have to make changes in pdb
file".<br>
<br>
<br>
When did I say that?<br>
<br>
<br>
Then How will I create .rtp file.<br>
<br>
<br>
That depends entirely upon what that residue is. Is it
a<br>
constituent residue of the protein, such that its
backbone is<br>
incorporated in the protein structure? Is it connected
via a<br>
sidechain? Or is it a ligand? Any or all of the
following might apply:<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/File_Formats/.rtp_File"
target="_blank">http://www.gromacs.org/Documentation/File_Formats/.rtp_File</a><br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/File_Formats/specbond.dat"
target="_blank">http://www.gromacs.org/Documentation/File_Formats/specbond.dat</a><br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Tutorials#General"
target="_blank">http://www.gromacs.org/Documentation/Tutorials#General</a>
(Drug-enzyme<br>
complex, although beware the use of PRODRG)<br>
<br>
And, of course, the manual, which describes the
contents of the .rtp<br>
file more thoroughly.<br>
<br>
-Justin<br>
<br>
29 Aralık 2010 19:32 tarihinde Justin A. Lemkul
<<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
</div>
<div>
<div class="h5"> <mailto:<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>> <mailto:<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>
yazdı:<br>
<br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Dear Justin,<br>
<br>
Thanks for your reply. Where is the error?<br>
<br>
Pdb file:<br>
<br>
ATOM 1 N ALA A 4<br>
ATOM 2 CA ALA A 4<br>
....<br>
ATOM 2688 N ALA B 4<br>
ATOM 2689 CA ALA B 4<br>
....<br>
ATOM 5449 OXT GLN B 361<br>
TER 5450 GLN B 361<br>
<br>
<br>
Right here. You're going from the end of
chain B to the<br>
beginning<br>
of chain A, then back to B later on. Also
realize that whatever<br>
"ABSG" or "BSG" is, it won't be recognized by
pdb2gmx unless<br>
you've<br>
built a proper .rtp entry for it.<br>
<br>
-Justin<br>
<br>
HETATM 5451 OAAABSG A 1<br>
HETATM 5452 OABABSG A 1<br>
....<br>
HETATM 5474 OAAABSG B 2<br>
HETATM 5475 OABABSG B 2<br>
....<br>
HETATM 5492 O HOH A 2<br>
HETATM 5493 O HOH A 362<br>
HETATM 5494 O HOH A 363<br>
....<br>
HETATM 5744 O HOH B 362<br>
HETATM 5745 O HOH B 363<br>
<br>
29 Aralık 2010 19:12 tarihinde Justin A.
Lemkul<br>
<<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<br>
</div>
</div>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>>
yazdı:
<div>
<div class="h5">
<br>
<br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Dear Mark,<br>
<br>
The chain identifier have
continuous. In sequence does<br>
not show<br>
any problem.<br>
<br>
<br>
<br>
Then you're not looking at the right
contents; pdb2gmx<br>
wouldn't<br>
complain otherwise. Usually HETATM
entries like HOH<br>
(water) are<br>
after all protein chains, so you might
have chains A,<br>
B, C,<br>
etc for<br>
protein followed by A, B, C, etc for
water. Have a<br>
more thorough<br>
look through the .pdb file.<br>
<br>
-Justin<br>
<br>
<br>
29 Aralık 2010 15:10 tarihinde Mark
Abraham<br>
<<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>><br>
<mailto:<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>>>>
yazdı:<br>
<br>
<br>
On 29/12/2010 10:12 PM, ahmet
yıldırım wrote:<br>
<br>
Dear users,<br>
<br>
ab@ubuntu:~/Desktop/3O87$
pdb2gmx -f 3O87.pdb<br>
-water tip3p<br>
<br>
Select the Force Field:<br>
5: OPLS-AA/L all-atom force
field (2001<br>
aminoacid<br>
dihedrals)<br>
<br>
Fatal error:<br>
Chain identifier 'A' was
used in two<br>
non-sequential blocks<br>
(residue 710, atom 54 49)<br>
<br>
What should I do to correct
this error?<br>
<br>
<br>
Look at the entries whose chain
identifier is<br>
A, and<br>
see why they<br>
are non-sequential, and take
suitable action to<br>
remedy. You<br>
may need<br>
to Google for the PDB file
format if you don't<br>
already<br>
understand it.<br>
<br>
Mark<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>
</div>
</div>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> <<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">http://vt.edu</a>> | (540) 231-9080
<div class="im"><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>
-- gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div>
<mailto:<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>
<div class="im"><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<br>
<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<br>
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>
</div>
<mailto:<a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>>.
<div class="im"><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>
<br>
<br>
<br>
<br>
-- <br>
Ahmet YILDIRIM<br>
</div>
</blockquote>
<div>
<div class="h5">
<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]<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 clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
</body>
</html>