Hi Allen,
If your heme group is attache to a CYS residue, then you can try using the
parameter mentioned in the trail of emails in the link.
Please follow the suggestions by AMBER experts if you face error similar to
what I did.
At the end I could generate the prmtop and inpcrd files necessary to begin
MD by following these suggestion.
I hope this helps.
cheers.
Vaibhav
http://archive.ambermd.org/201504/0114.html
On Fri, Jun 3, 2016 at 2:55 PM, 163邮箱 <zycz138.126.com> wrote:
> Hi,
>
> I have some questions about heme-contained protein. When I dealt with this
> kind of protein in tleap, I used the heme parameters provided by David A
> Case who had added NP and NO nonbond parameters to old HEM parametrization
> files. Unfortunately, CX nonbond parameters have not been provided, so I
> can not save the top files of the heme-contained protein. My question is
> how and from where I can get these parametrizations.
>
>
> The error obtain is written below:
>
> >sourcing: /home/zou/amber14//dat/leap/cmd/oldff/leaprc.ff99SB
> >source leaprc.gaff
> >loadamberparams heme.frcmod
> >loadamberprep Heme-all-atom.prep
> >HEM=loadpdb HEM.pdb
> > check HEM
> Checking 'HEM'....
> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
> Warning: Close contact of 1.451512 angstroms between .R<HEM 393>.A<HGM 64>
> and .R<HEM 393>.A<HP74 10>
> Checking parameters for unit 'HEM'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 2
> Unit is OK.
> > saveamberparm HEM HEM.prmtop HEM.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> For atom: .R<HEM 393>.A<CBB 32> Could not find vdW (or other) parameters
> for type: CX
> For atom: .R<HEM 393>.A<CBC 48> Could not find vdW (or other) parameters
> for type: CX
> Parameter file was not saved.
>
> Thank your for your help!
>
> Sincerely,
> Allen Zou
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With Regards.
Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK and
IISc, Bangalore)
Associate Professor,
Department of Pharmaceutical Chemistry,
School of Pharmacy & Technology Management,
SVKM's NMIMS,
Mukesh Patel Technology Park
Babulde, Bank of Tapi River,
Mumbai-Agra Road,
Shirpur, Dist. Dhule -425405
India.
Email: vaibhav.dixit.nmims.edu
www.nmims.edu
http://pharmacy-shirpur.nmims.edu/faculty-and-research/faculty/dr-vaibhav-dixit/
+91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Fri Jun 03 2016 - 04:30:02 PDT
