you mean to say i used these command on t-leap after changing the residue
name atom name according to .in file and frcmod file (is there any
automated way to change residue in the pdb file to escape from error or its
done manually)
loadamberparam hem_all.in
loadamberparam frcmod.hem
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
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Received on Wed Jun 28 2017 - 21:30:02 PDT
