[AMBER] no bonds formed between AA and non-standard residue

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Sun, 16 Feb 2020 20:30:32 +0900

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,
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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 - 07:30:02 PST
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