Dear Prof. Carlos SImerling and other experts,
I build the non-standard residue (Cys-Heme) by running G09 calculations and
esp file. The Cys was capped with N*Me* and CO-*H*.
Then I used antechamber to generate mol2 file and used -a gaff -nc -2 -m 6
options.
Then I edited the mol2 in xleap to delete capping atoms and kept only the
NHCH(CH2S)CO of the Cys and bonded the S and porphyrin Ns with Fe. This
gave me uncapped Cys-Heme mol2 using which I ran prmchk2 to generate frcmod
and added remaining missing parameters from SI of this paper
<
https://www.ncbi.nlm.nih.gov/pubmed/21997754>. That is why I was looking
for CYS and CYX parameters in the last 2-3 days.
Other people have parameterized heme and bonded the S to Fe, but I want to
parameterize the whole CYS-Heme and connect it with the rest of the
backbone using CYS's N and C atoms.
Please do give your valuable inputs on if this approach is reasonably
correct or not.
Thank you very much
On Sun, Feb 16, 2020 at 8:59 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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--
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
P Please consider the environment before printing this e-mail
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Received on Sun Feb 16 2020 - 08:30:03 PST
