thank you Elvis and Ross
now its look fine
On Thu, Jun 29, 2017 at 2:16 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
>
> Ok!! now I get it. The frcmod file had remarks extending to more line
> which is not allowed.
>
> I have deleted those lines and attached the edited frcmod file here.
>
>
> 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 11:37:18
> To: AMBER Mailing List
> Subject: Re: [AMBER] antechamber
>
> here are the files
>
> On Thu, Jun 29, 2017 at 1:56 AM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Hi Rana,
> >
> > I just saw your leap.log
> >
> > Unknown keyword: N.B.: para in parameter file. Perhaps a format error?
> > Unknown keyword: six-coo in parameter file. Perhaps a format error?
> > Unknown keyword: Force fiel in parameter file. Perhaps a format error?
> > Unknown keyword: Univers in parameter file. Perhaps a format error?
> > Unknown keyword: in parameter file. Perhaps a format error?
> > Unknown keyword: I modified in parameter file. Perhaps a format error?
> > Unknown keyword: addition o in parameter file. Perhaps a format error?
> >
> > These keywords are not known to me. Did you edit the frcmod file??
> Because
> > there are many illegal keywords as you see in the error.
> >
> >
> >
> >
> > 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
> > > >
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> >
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Received on Wed Jun 28 2017 - 23:30:05 PDT
