Elvis here is the leap.log file
i am confuse about this part after list
HEM gaff show
(check the residue the for Heme) my hem O2 file consist of HEM too
then
edit heme or whatever the name is
then display the atoms names in the new visualizer that opened.
Separately open the HEME-O2 pdb in pymol and label the atoms names.
On Thu, Jun 29, 2017 at 12:37 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> I am sure if there are any tutorials.
>
> But here is what I usually do.
>
> go to xleap then
>
> source leaprc.gaff
>
> loadamberparams heme.frcmod or whatever then name is
>
> loadamberprep hem.in or whatever the name is
>
> list
>
> (check the residue the for Heme)
>
> then
>
> edit heme or whatever the name is
>
> then display the atoms names in the new visualizer that opened.
>
>
> Separately open the HEME-O2 pdb in pymol and label the atoms names.
>
> Now compare the two atoms names and change the residue name and atom names
> to match the one in the xleap visualizer.
>
>
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>
>
> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> in/elvisadrianmartis/>
>
>
>
>
>
> ________________________________
> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> Sent: 29 June 2017 10:01:42
> To: AMBER Mailing List
> Subject: Re: [AMBER] antechamber
>
> Is there any tutorial with the help of that reference case i change my
> residue name in pdb file according to frcmod and .in files??
>
> On Wed, Jun 28, 2017 at 11:29 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > HI,
> >
> > As I have replied to the previous thread, systems with metal ions cannot
> > be directly used with antechamber. I have already provided you with the
> > frcmod and prepi files which you can directly use in leap but remember
> you
> > must rename your residue name and atom names in HEME to match in that in
> > the frcmod and prepi file.
> >
> >
> >
> > Best Regards
> >
> > [photo]
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry)
> > at Bombay College of Pharmacy
> >
> >
> > A Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> > Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
> >
> >
> > [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> > ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> > yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> > d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> > icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> > in/elvisadrianmartis/>
> >
> >
> >
> >
> >
> > ________________________________
> > From: Rana Rehan Khalid <rrkhalid.umich.edu>
> > Sent: 29 June 2017 04:07:12
> > To: AMBER Mailing List
> > Subject: [AMBER] antechamber
> >
> > hi Everyone
> >
> > i used antechamber for my heme fe--o2 ligand it show this error and mol2
> > not formed for heme-fe----O2. i also sending you the leap.log kindly tell
> > me where i am wrong
> >
> > Running: /home/rehan/Downloads/amber16/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > For atom[26]:O01, the best APS is not zero, bonds involved by this atom
> are
> > frozen
> >
> > For atom[45]:Fe, the best APS is not zero, bonds involved by this atom
> are
> > frozen
> >
> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic
> > double)Error: cannot run "/home/rehan/Downloads/amber16/bin/bondtype -j
> > full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jun 28 2017 - 22:00:05 PDT
