edit heme or whatever the name is
then display the atoms names in the new visualizer that opened.
i opened and label the atom name in pymol but how i do above two steps for
compare with pymol
On Thu, Jun 29, 2017 at 12:56 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> Elvis here is the leap.log file
> i am confuse about this part after list
>
> HEM gaff show
>
> (check the residue the for Heme) my hem O2 file consist of HEM too
>
> 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.
>
> 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-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 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
>> >
>> _______________________________________________
>> AMBER mailing list
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>>
>
>
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Received on Wed Jun 28 2017 - 22:30:02 PDT
