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-
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> 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
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Received on Wed Jun 28 2017 - 22:00:03 PDT
