Sed only gives a new string without rest of the pdb's so it should be
done in awk enterile but
all Stack-overflow could not solve it :-)
James
2017-08-04 21:00 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> 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 Mon Aug 07 2017 - 08:30:02 PDT
