Hello,
I am trying to use PRODRG to dock with an unnatual amminoacid and the site is not coming up. Is there a need address?
Are you referring to the PRODRG server?
It is not under our control I am afraid…
Oh ok. Is there an anlternative I can use to run my unnatural amino acid mutation?
I need to run PNS with a tyrosine on it, which I normally would have inputted into ProDrg for HADDOCK to recoginze it.
I need to run PNS with a tyrosine on it, which I normally would have inputted into ProDrg for HADDOCK to recoginze it.
Running a local version of HADDOCK?
Did you try submitting it to the HADDOCK server?
In that case the TYR should be defined also as HETATM and have the same residue name as PNS and unique atom names
This is HADDICK Server. I am currently getting the error when I did that.
There was an inconsistency in your data
Error message
Unable to generate topology for ligand PNS. PRODRG did not create the required output:
PRODRG> WARNING: deleted hydrogen HN from your input.
PRODRG> WARNING: deleted hydrogen HA from your input.
PRODRG> WARNING: deleted hydrogen HB2 from your input.
PRODRG> WARNING: deleted hydrogen HB3 from your input.
PRODRG> WARNING: deleted hydrogen H28 from your input.
PRODRG> WARNING: deleted hydrogen H29 from your input.
PRODRG> WARNING: deleted hydrogen H30 from your input.
PRODRG> WARNING: deleted hydrogen H31 from your input.
PRODRG> WARNING: deleted hydrogen H32 from your input.
PRODRG> WARNING: deleted hydrogen H33 from your input.
PRODRG> WARNING: deleted hydrogen H34 from your input.
PRODRG> WARNING: deleted hydrogen H35 from your input.
PRODRG> WARNING: deleted hydrogen H36 from your input.
PRODRG> WARNING: deleted hydrogen H37 from your input.
PRODRG> WARNING: deleted hydrogen H38 from your input.
PRODRG> WARNING: deleted hydrogen H39 from your input.
PRODRG> WARNING: deleted hydrogen H41 from your input.
PRODRG> WARNING: deleted hydrogen H42 from your input.
PRODRG> WARNING: deleted hydrogen H43 from your input.
PRODRG> WARNING: deleted hydrogen H44 from your input.
PRODRG> WARNING: deleted hydrogen H45 from your input.
PRODRG> WARNING: deleted hydrogen H46 from your input.
PRODRG> WARNING: deleted hydrogen H47 from your input.
PRODRG> WARNING: deleted hydrogen H48 from your input.
PRODRG> P is bonded to OG O1P O2P O3P C32
The hydrogen are not the problem - in any case it is better to remove them (will be added were needed)
But your phosphate seems to have too many bonds… Probably a rather distorted geometry of your ligand.
Did you ever get into PRODRG? I can’t find the address either.
Our web portal has a version in the backend