If you actually look at the second file and think for a moment, you may
see a problem. Think about how it differs from the other input files.
Here is how it starts:
------------
Force field modifcations for all-atom heme
N.B.: parameters around the iron atom are appropriate for a
six-coordinate (ligand bound) hemoglobin/myoglobin.
Force field parameters were adapted from D.A. Giammona, Ph.D. thesis,
University of California, Davis (1984).
---dac 12/90
I modified & added to dac's original set - C.Bayly 10/95
addition of NONBON parameters for NP and NO -- DAC,IA,RB 9/16
--------------
Bill
On 6/28/17 11:07 PM, Rana Rehan Khalid wrote:
> 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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Received on Wed Jun 28 2017 - 23:30:05 PDT
