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>> 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>>> 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>>>> 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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