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
>>>>>>>
>>>>> _______________________________________________
>>>>> 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
>
> _______________________________________________
> 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 - 09:30:05 PDT
