Hi,
As Bill suggested you will have to edit the pdb using a text editor to make changes.
Please use the frcmod and prepi files that Andrew has suggested in another thread.
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 11:12:20
To: AMBER Mailing List
Subject: Re: [AMBER] antechamber
when i load pdb file of hem then i find
two atom name new O01 and O02 that are two oxygen O2 bonded with Fe
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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 28 2017 - 23:00:03 PDT
