Hi Vaibhav,
Did you create a library file or bond the residue manually in tleap? Your
current setup doesn’t create a bond, and that type of bonding information
would not be in your frcmod file.
For example,
bond PDBID.RESID.ATOM PDBID.RESID.ATOM
This is commonly done with disulfides like so:
bond 4lyt.30.SG 4lyt.115.SG #from Amber constant pH tutorial
but can be done explicitly as well with other residues.
Clorice
On Sun, Feb 16, 2020 at 10:02 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear All,
> I'm using the attached pdb, mol2 and frcmod files in tleap and giving the
> following commands, but I can't see expected bonds in vmd.
> I have double checked that my usage in bond command is correct (at least to
> me).
> I get 1 non-fatal error and some warnings but when I save pdb the terminal
> residues don't appear to have bonded as then confirmed visually in vmd.
> Can you please suggest, why these bond commands are not working as
> expected?
> thank you.
>
> Here are my tleap commands.
> source leaprc.protein.ff14SB
> source leaprc.gaff
> loadamberparams frcmod.ionsjc_tip3p
> loadamberparams test-uncap1.frcmod
> HEM = loadmol2 test-uncap1.mol2
> 3v8d = loadpdb 3v8d-test7.pdb
>
>
>
> Warning: Close contact of 1.370191 angstroms between .R<GLU 447>.A<HB2 6>
> and .R<ALA 450>.A<HA 4>
> Checking parameters for unit '3v8d'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 1 Warnings: 25
>
> *> bond 3v8d.482.C3 3v8d.421.N> bond 3v8d.420.C 3v8d.482.N1*
> > saveamberparm 3v8d test.prmtop test.rst7
> Checking Unit.
>
> Warning: There is a bond of 4.825647 angstroms between:
>
> Warning: The unperturbed charge of the unit (3.077800) is not integral.
>
> Warning: The unperturbed charge of the unit (3.077800) is not zero.
>
> Note: Ignoring the error and warnings from Unit Checking.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 1612 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CHIE 1
> CILE 1
> HEM 1
> NPRO 1
> NSER 1
> )
> (no restraints)
> > savepdb 3v8d 3v8d-tleap.pdb
> Writing pdb file: 3v8d-tleap.pdb
>
> Warning: Converting N-terminal residue name to PDB format: NSER -> SER
>
> Warning: Converting C-terminal residue name to PDB format: CILE -> ILE
>
> Warning: Converting N-terminal residue name to PDB format: NPRO -> PRO
>
> Warning: Converting C-terminal residue name to PDB format: CHIE -> HIE
> > quit
> Quit
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7
> <https://www.google.com/maps/search/ster,+131+Princess+Street,+Manchester+M1+7?entry=gmail&source=g>DN,
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Received on Sun Feb 16 2020 - 07:30:03 PST
