You might want to try 'sed' instead.
Bill
On 8/4/17 11:50 AM, James Starlight wrote:
> BTW could someone help me with the scripting of such CAPPING?
> For the pdb I need to 1) find the string where the 3rd column = OXT,
> change it to N and the residue name (4 column to NHE), and also the
> last column from O to N; 2) change the next string to TER
>
> I tried to use
>
> awk '$3=="OXT"{ f=1; rn=NR; $3=$NF="N"; $4="NHE" }/TER/ && f && NR-rn
> == 1{ $0=$1 }1' file.pdb
>
> it produce correct substitution, however put only one spacing between
> columns of new string like:
>
> ATOM 2410 N NHE 299 -17.563 -15.711 -15.915 1.00 76.42 N
> TER
>
> thus producing broken pdb file. How to present the original format?
>
> ATOM 2448 N NHE 301 -6.821 36.580 65.884 1.00 19.70 N
> TER
>
>
>
> Thanks!!
>
> James
>
> 2017-08-04 14:34 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>> Yep that's right! (sorry i am stupid)
>> So the problem just disapears if I
>> 1) remove OXT in pdb (the tleap than add it back without error)
>> 2_ substitute OXT for N of NHE (add peptide bond of cap) - tleap again
>> add everything back.
>>
>> The same for all pdbs prepared by Modeller
>>
>> James
>>
>> 2017-08-04 14:04 GMT+02:00 David A Case <dacase.chem.rutgers.edu>:
>>> On Fri, Aug 04, 2017, James Starlight wrote:
>>>
>>>> Yep it was the C-term residue and the TER was present
>>> Then something strange is happening. We would need to see a minimal example
>>> that illustrates the problem. Try to see what is different about your
>>> protein PDB (or tleap input commands) compared to standard examples that
>>> don't exhibit this problem.
>>>
>>>> So to fix the issue I made a script which changes OXT of last residue
>>>> to N of NHE (add NHE to cap C term)
>>>> and also change N of the first residue to C of ACE (tleap than add
>>>> back N for the adjacent residue and surprisingly fixed steric clashes
>>>> between N and C of ACE). I checked in VMD the new peptide bonds look
>>>> fine.
>>>>
>>>> There is no bugs with charges and any warning. Total charge of the
>>>> system =0 after its neutralization. BUT total charge of the system
>>>> has not been changed compared to uncapped case....
>>> Sounds exactly like what one expect, does it not? If you neutralize both
>>> the N- and C-terminal residues, then the total charge of the protein/peptide
>>> will not change.
>>>
>>> ....dac
>>>
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Received on Fri Aug 04 2017 - 12:30:02 PDT
