You don't say how you built the non standard residue. The leap output
doesn't really tell us your while workflow. If you used gaff, you'll need
cross terms for the bonded parameters between gaff and ff14SB, or something
else depending on what you used.
Also in Vmd make sure you are not evaluating bonds based on the pdb. You
must load the prmtop and coordinates from leap in order to display the
bonds present in the prmtop file.
On Sun, Feb 16, 2020, 10:01 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 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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Received on Sun Feb 16 2020 - 07:30:03 PST
