Dear Amber community members
Thanks a lot Jio for those suggestions.
But there are some doubts.
1) The heme that I'm considering has two additional ligands S of Cys442 and
a water molecule.
Should I not consider them while defining parameters (the heme set that you
suggested has no parameters for the Fe-S and Fe-O interactions)?
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
2) Is it correct to consider whole of Fe-porphyrin and water as part of
residue CYS442 while making lib files? i.e. to define it as non-standard
residue.
3) If yes then the heme set suggested on the site is not probably correct
for the case at hand !!!
4) Then how do I get resp charges for the same (as antechamber is not
working on gaussian output)?
Finally is there another better approach for this general issue of handling
heme in CYP MD studies????
Please find time and see if you can comment on these issues.
Thanks in advance and waiting for comments and suggestions...
On Sat, Jun 19, 2010 at 11:33 PM, Jio M <jiomm.yahoo.com> wrote:
> Hi
>
> 1) Antechamber cannot handle Fe or other metals(somebody pls correct me if
> I m wrong)
>
> 2) For parameters you can follow some publications but note the units they
> are using or in this link http://www.pharmacy.manchester.ac.uk/bryce/amber
>
> 3) for water I dont know
>
> --- On Sat, 6/19/10, vaibhav dixit <vaibhavadixit.gmail.com> wrote:
>
> From: vaibhav dixit <vaibhavadixit.gmail.com>
> Subject: [AMBER] antechamber issue and parameters for heme of cyp3a4
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Saturday, June 19, 2010, 5:00 AM
>
> Dear Amber community members,
> Thanks a lot for your suggestions and comments earlier.
>
> Using the advanced tutorial for non-standard residues, I'm trying to
> prepare
> library for heme residue.
> http://ambermd.org/tutorials/advanced/tutorial1_adv/
> I'm using 2jod.pdb and considering Fe-porphyrin and one co-ordinated water
> molecule as part of the residue CYS442. Is this a good approximation?
>
> I have calculated esp potential for the same using Gaussian03 for the
> crystal structure geometry.
> But the antechamber is not working properly with the following error.
> The lib file generated (cyx.lib.txt) and non-standard residue with Heme
> cystein and water (heme_cyx_w.pdb) are attached.
> Please find time and see if you can suggest some solution for the same.
> Is there another approach to deal with the same issue of handling Heme
> residues for performing MD studies on CYPs.
>
> Waiting for your comments and thanks in advance...
>
> The error with antechamber:
> --------
> [vaibhav.localhost 1tqn]$ antechamber -i heme_cys_w.gout -fi gout -o
> heme_cys_w.prep -fo prepi -c resp
>
> For atom[7]:Fe1, the best APS is not zero, bonds involved by this atom are
> frozen
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly
> increase the computer time
> Error: cannot run "/home/vaibhav/software/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
> ----------
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D. Scholar
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
>
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>
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--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Sat Jun 19 2010 - 21:30:05 PDT
