Hi,
What are the exact error/warning messages your are getting from leap?
-Dan
On Tue, Feb 13, 2018 at 2:22 AM, Sivasudhan R <sivasudhan.rath.gmail.com> wrote:
> Dear Amber users,
> I am a novice user with Antechamber. I have a system in which the ligand (76 atoms, with netcharge -1) is covalently connected to the protein (CYS:SG).
> I am interested in generating a parameter file for protein+ligand (complex) . I could generate .prmtop and .inpcrd files for the ligand separately. The problem occurs when I try for the complex!
>
> Used pd4amber —reduce , [removed ligand coord] and added a hydrogen (for protonation) and a capping hydrogen (H33) > ligand-capped.pdb : Netcharge -1 /singlet
>
> During the parametrization of the ligand (a non-standard residue) :
> antechamber -i lig.log -fi gout -fo ac -o lig.ac -c resp -nc -1 -rn LIG -at gaff
>
> I have prepgen file
> [to remove capping H and to tell that it will be connected to CYS of the protein]
> Lig.mc
> HEAD_GROUP C24
> OMIT_NAME H33
> PRE_HEAD_TYPE SG
> CHARGE -1.0
>
> prepgen -i lig.ac -m Lig.mc -o lig.prepin -f int (I get NEWPDB.PDB , using this as a reference PDB for ligand)
>
> parmchk -i lig.prepin -f prepi -o lig.frcmod
>
> In leap:
> source leaprc.gaff
> source leaper.protein.ff14SB
> Loadamberprep lig.prepin
> Loadamberparams lig.frcmod
> x = loadpdb complex.pdb
> desc x.297.C24. (of ligand)
> desc x.2.SG. (of protein: (tleap adds additional H, filling the valence of CYS 2:SG))
> bond x.297.C24 x.2.SG
> saveoff x complex.lib
> Loadoff complex.lib
> saveamberparm x complex.prmtop complex.inpcrd
>
> I get an error saying atomtypes are missing. I also manually edited the PDB (the ligand part) with no success . I am not sure, if my procedure was correct.
>
> Also, I would like to know the protocol for changing the atom type of subset of atoms (ligand) in a complex.pdb Is the bonding step required (I do it because, in the prepgen, after omitting the H33, it said use bond command to bond) given that I load a complex.pdb (where the protein and ligand are bonded)
>
> Kindly help.
>
> Thank you,
>
>
> Sincerely,
>
> Sivasudhan R
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Feb 13 2018 - 06:00:04 PST
