Does the HEM template have O's that match? If so, change the atom names
in the pdb to match.
E.g. 'savepdb HEM hem.pdb' in tleap or 'edit HEM' in xleap to see atom
names in position.
Hopefully those atoms are O1A and O2A.
If not, maybe your pdb is for a different HEM molecule.
Bill
On 6/28/17 11:27 PM, Rana Rehan Khalid wrote:
> 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
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>>>> _______________________________________________
>>>> AMBER mailing list
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>>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
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Received on Thu Jun 29 2017 - 00:00:03 PDT
