Thanks, I will look into!
Actually what I do need is just add neutral caps to the N (ACE) and C
(NHE) term residues via some modification of the input pdb. Here I
have described the trick of atom modifications which are recognized by
tleap. So if would be great if someone here propose a script in any
format which is possible to integrate into the bash.
James
2017-08-07 18:29 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> parm file.pdb
> trajin file.pdb
> ...
> trajout out.pdb
>
> Some tutorials: http://ambermd.org/tutorials/#analysis
>
> -Dan
>
> On Mon, Aug 7, 2017 at 12:28 PM, James Starlight <jmsstarlight.gmail.com> wrote:
>> 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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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>
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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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>>
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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 - 11:30:02 PDT
