Hi,
It seems that I have to load a pdb into cpptraj to pre-process it
before sending to tleap, right? Where is possible to look for the
tutorial - I have used cpptraj only for the analysis of the
trajectories..
James
2017-08-07 18:13 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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
>>>>>>
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>
>
> --
> -------------------------
> 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
>
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Received on Mon Aug 07 2017 - 09:30:04 PDT
