Dear Prof. Case and All,
thanks for the reminder and your response.
I move HEM to the end and used pdb4amber to get better PDB file.
Using this and frcmod shared by Sason Shaik's group, pmrtop/inpcrd are
generated, but tleap warns about residues not being connected to the main
chain.
I think cysteine not being connected to the protein backbone is not correct.
So these prmtop/inpcrd fiels don't represent the protein correctly.
Did I understand the following tleap message (in *bold*) correctly?
I would be grateful if HEM parameter experts/authors on the list can
comment and make suggestions on this issue.
Thank you all.
regards
Marking per-residue atom chain types.
* (Residues lacking connect0/connect1 - these don't have chain types
marked:*
res total affected
* **** * 1
CASP 1
CYP 1
NGLY 1
NILE 1
WAT 13994
)
(no restraints)
On Fri, May 31, 2019 at 6:30 PM David A Case <david.case.rutgers.edu> wrote:
> On Fri, May 31, 2019, Vaibhav Dixit wrote:
>
> >Dear Prof. Case,
>
> Please send amber-related questions to the mail reflector,
> amber.ambermd.org,
> and not to me personally. That way, many people can see your question and
> try
> to help, and the answers can help others with similar questions. See
> http://lists.ambermd.org/mailman/listinfo/amber for information on how to
> subscribe.
>
> In particular, Tom Cheatham and others follow the mailing list, and can
> probably help.
>
> >In another attempt, I used CYX and didn't connect S-Fe.
>
> You may have to use the "bond" command in tleap to add missing bonds.
>
> >> 1) I removed the atoms causing the error from the PDB, and created bonds
> >> connecting residues 417-418-419 (since 418 is CYP non-standard
> cysteine),
> >> prmtop, inpcrd fails to generate.
>
> >> Error: Could not find bond parameter for: C - N3
> >> Checking for angle parameters.
> >> Error: Could not find angle parameter: O - C - N3
> >> Error: Could not find angle parameter: C - N3 - H
> >> Error: Could not find angle parameter: C - N3 - H
> >> Error: Could not find angle parameter: C - N3 - H
> >> Error: Could not find angle parameter: C - N3 - CX
> >> Error: Could not find angle parameter: CT - C - N3
>
> I don't know why these are missing....is there an N3 atom type in CYP?
> Are you sure there is no frcmod file you are failing to load?
>
> In options 2, I wouldn't worry about the ****, but be sure to use parmed
> to check that you indeed have a bond between the CYP and Fe (as well as
> other bonds that you need.
>
> ...dac
>
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 31 2019 - 12:30:02 PDT
