Hi,
You could try the GitHub version of cpptraj. It will automatically
generate TER cards for PDBs based on molecule information, and you can
change atom or residue names with the new "change" command.
-Dan
On Mon, Aug 7, 2017 at 11:00 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 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
>>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 07 2017 - 09:30:03 PDT
