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 - 22:00:04 PDT
