Dear all,
this topic may be merged with Nucleic acids docking, i have read but i didnot get my answer from that topic.
i have the following queries
- my dsRNA structure was not built by 3d-Dart, since it is deleting URI bases in sequence, so i use make-na server for structure construction.
i have two chain of RNA named chain C (residue numbered 1-46) & chain D (residue numbered 47-92).
when i checked with (pdb-tools by Dr.João Rodrigues) pdb_format.py script, its showing the the following error (only in base 90, 91 and 92) posted as image below.
kindly tell me how to rectify this error in pdb file to use in haddock for docking with protein dimer.
i donot have that much computer language knowledge.
thank you
Hello,
My guess is that these lines have been added externally and does not contain the 3 last columns required for a proper PDB. These 3 columns are the 78, 79 and 80th character of each ATOM lines and can contain the element (77-78) and the charge (79-80) of the atom. WE sometimes also use this column to add a segid information.
In any case, information within these columns is optional and you can leave them blank but you need to keep space for them in your PDB file.
You can find extra information on the PDB format here: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
I hope this will help,
Mikael
Dear Dr.mtrellet,
Thank you for your reply. how can i rectify these errors in pdb file to use in haddock. kindly tell me how to fix it.
- I donot have knowledge in editing it. it will be great if u help me to edit this pdb file.
- Is there some other way to do this.
thank u
Did you even try to submit it to the web server? Our server should be able to handle the missing three columns, if this is really the problem.
Anyway, the format of your PDB file does not match with the standard (either spaces are missing or indeed the last three columns have been deleted). You can edit your file with any text editor of your choice (not Word). Save it as text file and upload it to HADDOCK.
Dear Dr.Adrimel,
thanks for the advice, i have submitted the file without editing missing column, haddock has accepted the file format and its running.
i have few query regarding creating specific restraint via haddock server generating TBL files.
for docking homodimer with double stranded RNA. homodimer protein chain A & B; and dsRNA chain C & D
Example : protein chain A- residue His18 and Lys20 interact with sugar phosphate backbone of dsRNA base chain C of (Cyt residue no-7) - OP1 group, and Uri (residue no-21) O2’ group respectively. how to mention this in TBL generate server.
in active residue whether only number has to be written or we can mention the active group invovlied in interaction like OP1, O2’ with the number, if so kindly tell me how to mention in active residue box. i use to mention only number like (Active residue - 18,20).
my docking is not targeted to area of interest, so pls help me.
very big thanks for Haddock groups, support and help
thank u
I suggest you start reading carefully our Nature Protocol 2010 paper - there are examples of restraints in it
Also check carefully the topics about dimeric system in this site
Dear Dr. amjjbonvin,
sir i read that paper, box4 - has restraints format.
kindly clarify these queries
- suppose whether i can type in the notepad, the format mentioned in nature protocol and save as .tbl file (or) directly use the notepad to upload it in server.
- mostly i will incorporate the X-ray crystallographic data of homologous interactome complex, which type of restraint will be useful, a) whether hydrogen bond detail will be entered in hydrogen bond restraint?. b) non-bonded restraint will be entered in which restraint?
thank u sir
- suppose whether i can type in the notepad, the format mentioned in nature protocol and save as .tbl file (or) directly use the notepad to upload it in server.
It should be uploaded as a separate text file to the server (distance restraints menu - expert interface)
- mostly i will incorporate the X-ray crystallographic data of homologous interactome complex, which type of restraint will be useful, a) whether hydrogen bond detail will be entered in hydrogen bond restraint?
It can - or in any other distance restraints.
b) non-bonded restraint will be entered in which restraint?
What do you mean by that?
Dear Dr. amjjbonvin,
sir,
now i face only one problem, to the homodimer protein, the dsRNA is not binding to both the protein monomer as in x-ray structure, but bind to single monomer one sided. since u have suggested to add more restraint in the discussion of “nucleic acid docking title”. i wanted to add specific atom restraint as mentioned below, targeting protien to bind sugar phosohate backbone.
-
sir i refer “non-bonded restraint” to non-bonded contact (van der Waals
bonds) from bond file of nucplot.
EX :
protein DNA Distance
HIS A 539 CA C D 23 OP1 3.11
HIS A 539 CB C D 23 OP1 2.69
HIS A 539 CG C D 23 OP1 3.07
HIS A 539 ND1 C D 23 OP1 2.88
ARG A 544 NH1 G C 27 O2’ 3.16
ARG A 544 NH2 C C 28 C5’ 3.03
ARG A 544 NH2 C C 28 C4’ 3.14
-
In which restraint option it has to be entered, how to enter this restraint ?
-
if this have to be entered in dihedral restraint, then how to get the < force
constant> < target dihedral angle> < error range> < exponent>? .
thank u
- sir i refer “non-bonded restraint” to non-bonded contact (van der Waals
bonds) from bond file of nucplot.
EX :
protein DNA Distance
HIS A 539 CA C D 23 OP1 3.11
HIS A 539 CB C D 23 OP1 2.69
…
Simply then define distance restraints for those atom pairs.
But if you want to reproduce an existing complex, you might as well try to superimpose the components on the complex and then refine the model.
• In which restraint option it has to be entered, how to enter this restraint ?
As unambiguous restraints (expert level - distance restraints menu)
• if this have to be entered in dihedral restraint, then how to get the < force
constant> < target dihedral angle> < error range> < exponent>? .
force constant can simply be 1 and the exponent 2 - the target dihedral angle you will have to define what you have.
Dear Dr. amjjbonvin,
sir,
For ex :
protein DNA Distance
HIS A 539 CA C D 23 OP1 3.11
for above interaction between HIS 539, chain A and DNA- CYT 23, chain D, phosphate, with bond distance - 3.1, whether i can assign syntax as given below in distance restraint file format.
assign (resid 539 and segid A and name CA)
(resid 23 and segid D and name OP1) 3.1 3.1 0.0
thank u sir
Yes - but I would give a bit more range to the distance in that case, e.g. adding 0.2-0.5A to it
Dear Dr. amjjbonvin
thank u sir. i will do it as per ur instruction.
thank u very much for ur patience reply.
