Have you tried loading structures separately and combining them in tleap?
ligand=loadmol2 ligand.mol2
protein=loadpdb protein.pdb
complex=combine {ligand protein}
saveamberparm complex x.prmtop x.rst7
Busra Demir
Bionanodesign Laboratory, TOBB ETU
Sogutozu/Ankara
On Mon, 17 Feb 2020, 08:56 Vaibhav Dixit, <vaibhavadixit.gmail.com> wrote:
> Dear All,
> The vmd shows the lack of bonds upon loading prmtop and rst7 files
> (attached compressed image).
> Thus the expected connection (bond) was not created even after giving
> correct atom-residue information as shared in earlier email.
> Can someone please suggest on how to fix this problem?
> Also I'm getting errors while writing pdb using ambpdb with -conect option.
> thank you.
>
> ambpdb -p test.prmtop -c test.rst7 -conect > 3v8d-test8.pdb
> Error: Atom 7779 was assigned a lower molecule # (1) than previous atom
> (2).
> Error: This can happen if bond information is incorrect or missing, or if
> the
> Error: atom numbering in molecules is not sequential. Try one of the
> Error: following:
> Error: - If this is a PDB file, try using the 'noconect' keyword.
> Error: - If this topology did not have bond info, try increasing the bond
> Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
> Error: - Use the 'fixatomorder' command to reorder the topology and any
> Error: associated coordinates.
> Error: - Use the 'setMolecules' command in parmed to reorder only the
> Error: topology.
> Error: Could not determine molecule information for test.prmtop.
> Error: SetSolventInfo: No molecule information.
> Error: Could not determine solvent information for test.prmtop.
>
> On Mon, Feb 17, 2020 at 3:55 AM Busra Demir <bdemir09.gmail.com> wrote:
>
> > Hi Vaibhav,
> >
> > This is probably about VMD itself. It has cutoff distance to describe a
> > bond.
> > You should load both .prmtop and .inpcrd files to be sure of leap
> bonding.
> >
> > Best,
> >
> > Busra Demir
> > Bionanodesign Laboratory, TOBB ETU
> > Sogutozu/Ankara
> >
> >
> > On Sun, Feb 16, 2020 at 7:28 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> > wrote:
> >
> > > 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
> > >
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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 Mon Feb 17 2020 - 00:30:02 PST
