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>
<br>Thanks in advance<br><br><div class="gmail_quote">29 Aralık 2010 20:07 tarihinde Justin A. Lemkul <span dir="ltr"><<a 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 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 href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a 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 href="http://www.gromacs.org/Documentation/File_Formats/.rtp_File" target="_blank">http://www.gromacs.org/Documentation/File_Formats/.rtp_File</a><br>
<a 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 href="http://www.gromacs.org/Documentation/File_Formats/specbond.dat" target="_blank">http://www.gromacs.org/Documentation/File_Formats/specbond.dat</a><br>
<a 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 href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a 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 href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<br></div></div>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>> yazdı:<div><div></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 href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a 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 href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a 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>
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<br>
-- <br>
Ahmet YILDIRIM<br>
</div></blockquote><div><div></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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a 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>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>