PRODRG server sometimes assigns CR61 for aromatic carbons and sometimes assigns CR1, CR0 for my ligand. What is the difference between the two? Where can I get more info on the atom types used in prodrg apart from the published prodrg articles?
Hi Chandrakala,
You can directly contact to Daan Van Aalten Laboratory. Here is the weblink to his Laboratory.
http://davapc1.bioch.dundee.ac.uk/new/index.html
I made a few trial calculations.
(a) When we submit a .pdb file then the prodrg does a unified atom calculation of carbon and proton together in the rings and assigns a type CR61 and CB. CR61 the mass will hence be 13.019 and is the carbon that has a proton attached to it. Carbons which are attached to heteroatoms other than proton are denoted as CB. The mass here is 12.0110
(b) When the molecule is drawn using JME or text drawing it uses the CR1 or CR0 notations. CR1 is the carbon to which a proton is attached. CR0 is the carbon which is bonded to a heteroatom other than a proton. In this case the mass of all carbons are 12.0110
Test it yourself with a pdb file you have of a known compound. and then draw the compound and compare the outputs
I did not write to Daan Van Aalten because now it seemed obvious and I would not want to write as things seem clear to me know. test it!!!
As for my knowledge the docking programs uses very simplified force fields and often gives inaccurate results. And there are lots of differences and disparities in the modeling of different docking programs. So it is better to contact the software vendor or some docking expert directly.
i also faced similar problems, i want t build and rectify the topologies from the PRODRG. but how can i buid this
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