I recommend using a text editor and making the substitution globally in
the pdb.
Bill
On 6/28/17 9:31 PM, Rana Rehan Khalid wrote:
> 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
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Jun 28 2017 - 22:00:06 PDT
