ahmet yıldırım wrote:
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.
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.
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
-Justin
Thanks for your help
29 Aralık 2010 19:49 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> yazdı:
ahmet yıldırım wrote:
You said "You do not have to make changes in pdb file".
When did I say that?
Then How will I create .rtp file.
That depends entirely upon what that residue is. Is it a
constituent residue of the protein, such that its backbone is
incorporated in the protein structure? Is it connected via a
sidechain? Or is it a ligand? Any or all of the following might apply:
http://www.gromacs.org/Documentation/File_Formats/.rtp_File
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
http://www.gromacs.org/Documentation/File_Formats/specbond.dat
http://www.gromacs.org/Documentation/Tutorials#General (Drug-enzyme
complex, although beware the use of PRODRG)
And, of course, the manual, which describes the contents of the .rtp
file more thoroughly.
-Justin
29 Aralık 2010 19:32 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>> yazdı:
ahmet yıldırım wrote:
Dear Justin,
Thanks for your reply. Where is the error?
Pdb file:
ATOM 1 N ALA A 4
ATOM 2 CA ALA A 4
....
ATOM 2688 N ALA B 4
ATOM 2689 CA ALA B 4
....
ATOM 5449 OXT GLN B 361
TER 5450 GLN B 361
Right here. 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, it won't be recognized by pdb2gmx unless
you've
built a proper .rtp entry for it.
-Justin
HETATM 5451 OAAABSG A 1
HETATM 5452 OABABSG A 1
....
HETATM 5474 OAAABSG B 2
HETATM 5475 OABABSG B 2
....
HETATM 5492 O HOH A 2
HETATM 5493 O HOH A 362
HETATM 5494 O HOH A 363
....
HETATM 5744 O HOH B 362
HETATM 5745 O HOH B 363
29 Aralık 2010 19:12 tarihinde Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> yazdı:
ahmet yıldırım wrote:
Dear Mark,
The chain identifier have continuous. In sequence does
not show
any problem.
Then you're not looking at the right contents; pdb2gmx
wouldn't
complain otherwise. Usually HETATM entries like HOH
(water) are
after all protein chains, so you might have chains A,
B, C,
etc for
protein followed by A, B, C, etc for water. Have a
more thorough
look through the .pdb file.
-Justin
29 Aralık 2010 15:10 tarihinde Mark Abraham
<mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>>> yazdı:
On 29/12/2010 10:12 PM, ahmet yıldırım wrote:
Dear users,
a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb
-water tip3p
Select the Force Field:
5: OPLS-AA/L all-atom force field (2001
aminoacid
dihedrals)
Fatal error:
Chain identifier 'A' was used in two
non-sequential blocks
(residue 710, atom 54 49)
What should I do to correct this error?
Look at the entries whose chain identifier is
A, and
see why they
are non-sequential, and take suitable action to
remedy. You
may need
to Google for the PDB file format if you don't
already
understand it.
Mark
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Ahmet YILDIRIM
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
