In fact, it looks like an email text is being used as a parameter file.
Bill
On 6/28/17 10:56 PM, Elvis Martis 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 - 23:00:04 PDT
