sorry, for typo. I still *can't *see the bonds in vmd.
On Mon, Feb 17, 2020 at 6:41 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear All.
> As suggested by David, I tried parmed on prmtop/rst7 files.
> It give 3 warnings for long bonds, one is between ILE420 and HEM which I
> did connect using the bond commands shown at the bottom (leap.log
> attached). But I can see these bonds in vmd, where I see terminal ProNH2
> and ILECOO (as attached earlier).
> Parmed doesn't mention residue number for 1st warnning for CYSs (I don't
> think there is a disulfide bond in this protein, 3v8d). I wasn't expecting
> the 3rd error as well, I had build 3 missing residue by overlapping/copying
> these from 3sn5 for the same protein CYP7A1 (all other residues were
> present, I'm hoping tleap will build any missing atoms for all of them give
> backbone coords).
>
> tleap log doesn't contain any errors after bond commands. It has some
> warnings for missing improper torsions (it wrote the prmtop/rst7 files
> anyway, should I be concerned about this?).
> The result is the same even if I create a complex out of separate ligand
> protein files or load a complexed pdb.
> Please suggest further so that I can be sure that modified residue
> (CYS-HEM) is connected to the main chain.
>
> (base) [exx.c107739 xleap-mol2]$ parmed -p com.prmtop -c com.rst7
>
> /^^^/ /]
> / ] / ]
> _______/ ]___ / ]
> / \_____/ /
> _/ [@] \ \ \
> /.. | | ]
> VVVvvv\ | | _/\ ]
> P A R M E D | / \ ]
> AAA^^^^^ / \]
> \_________\ \_____/
> \ \
> \____\
>
> ParmEd: a Parameter file Editor
>
>
> Loaded Amber topology file com.prmtop with coordinates from com.rst7
>
> Reading input from STDIN...
> > checkvalidity
> Determining validity of prmtop
> 3 total warnings
>
> MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
> within 3
> Angstroms. Rename CYS to CYX in the PDB file and use the
> 'bond' command in tleap to create the disulfide bond
>
> LongBondWarning: Atoms 6742 (ILE 420 [N]) and 7793 (HEM 482 [C3]) are
> bonded
> (equilibrium length 1.379 A) but are 4.898 A apart. This
> often
> indicates gaps in the original sequence and should be
> checked
> carefully.
>
> LongBondWarning: Atoms 7256 (GLN 449 [C]) and 7258 (ALA 450 [N]) are
> bonded
> (equilibrium length 1.335 A) but are 4.826 A apart. This
> often
> indicates gaps in the original sequence and should be
> checked
> carefully.
>
> >
>
> *tleap commands:*
> source leaprc.protein.ff14SB
> source leaprc.gaff
> loadamberparams frcmod.ionsjc_tip3p
> loadamberparams test-uncap1.frcmod
> HEM = loadmol2 test-uncap3.mol2
> 3v8d = loadpdb 3v8d-prep.pdb
> com = combine { 3v8d HEM }
> bond com.482.C3 com.420.N
> bond com.419.C com.482.N1
> saveamberparm com com.prmtop com.rst7
>
>
> On Mon, Feb 17, 2020 at 9:38 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Mon, Feb 17, 2020, Vaibhav Dixit wrote:
>>
>> >Even after combine option followed by bond commands, the expected bonds
>> are
>> >not generated as seen in vmd.
>>
>> First: use parmed to check for bonds: then it's easy to report exactly
>> what you did to the list.
>>
>> Second: double check that there were no errors from tleap arising from
>> the bond commands.
>>
>> Then: post as simple an example as you can, show exactly what bond
>> command(s) you used in tleap, and what commands and results you got from
>> parmed when you interrogated the resulting prmtop file.
>>
>> ....dac
>>
>>
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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
>
>
--
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 - 05:30:02 PST
