after that i loadpdb then it gives msg
"""The file contained 2 atoms not in residue templates"""
Created a new atom named: O01 within residue: .R<HEM 187>
Created a new atom named: O02 within residue: .R<HEM 187>
total atoms in file: 45
Leap added 30 missing atoms according to residue templates:
30 H / lone pairs
it mean i have to change these two atom name from the pdb file
On Thu, Jun 29, 2017 at 2:23 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> 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-wqOl
>> XSGjbmEyga9C8lmU1bs-_yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473
>> lEq28nSHQ=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.elvismar
>> tis.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
>> >
>>
>> _______________________________________________
>> AMBER mailing list
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>>
>>
>
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Received on Wed Jun 28 2017 - 23:30:06 PDT
