Hello Gromacs Users, I have been trying to run a simulation of PTM residues which has NAG, BMA, MAN, etc glycosylated residues in my protein. First, I would like to ask does anyone has .hdb file for such molecules for charmm22* or charmm36 ff as I am having following error:
*WARNING: atom H1 is missing in residue NAG 2345 in the pdb file* * You might need to add atom H1 to the hydrogen database of building block NAG* * in the file merged.hdb (see the manual)* *WARNING: atom O1 is missing in residue NAG 2345 in the pdb file* *WARNING: atom HO1 is missing in residue NAG 2345 in the pdb file* * You might need to add atom HO1 to the hydrogen database of building block NAG* * in the file merged.hdb (see the manual)* *WARNING: atom H5 is missing in residue NAG 2345 in the pdb file* * You might need to add atom H5 to the hydrogen database of building block NAG* * in the file merged.hdb (see the manual)* *WARNING: atom H2 is missing in residue NAG 2345 in the pdb file* * You might need to add atom H2 to the hydrogen database of building block NAG* * in the file merged.hdb (see the manual)* *WARNING: atom HN is missing in residue NAG 2345 in the pdb file* * You might need to add atom HN to the hydrogen database of building block NAG* * in the file merged.hdb (see the manual)* I do have a .rtp pertaining to its bonds, impropers, atoms but just to make it future-proof to use pdb2gmx, I would like to have it. Cheers, Vishal -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
