One more question here regarding capping and tleap:
when I add C atom of ACE cap on the place of N atom of the 1st
residue, theap than build all missing atoms of ACE and the N of the
1st residue:
ATOM 1 HH31 ACE 1 5.640 -15.680 25.039 1.00 0.00
ATOM 2 CH3 ACE 1 5.248 -16.697 25.039 1.00 0.00
ATOM 3 HH32 ACE 1 5.596 -17.221 25.928 1.00 0.00
ATOM 4 HH33 ACE 1 5.596 -17.221 24.149 1.00 0.00
ATOM 5 C ACE 1 3.718 -16.697 25.039 1.00 0.00
ATOM 6 O ACE 1 3.094 -15.638 25.039 1.00 0.00
ATOM 7 N CYX 2 3.737 -16.735 25.055 1.00 0.00
ATOM 8 H CYX 2 4.076 -15.790 24.947 1.00 0.00
ATOM 9 CA CYX 2 4.542 -17.818 24.527 1.00 0.00
...
But there is a steric clash between N and C atoms of ACE and CYX:
WARNING: There is a bond of 0.045398 angstroms between:
------- .R<ACE 1>.A<C 5> and .R<CYX 2>.A<N 1>
A question: Is it possible to relax the selected two amino-acids like in Xleap ?
Thanks!
James
2017-08-07 20:07 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> 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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>>>>>>> AMBER.ambermd.org
>>>>>>> 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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>>
>>
>> --
>> -------------------------
>> 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 Wed Aug 09 2017 - 02:30:03 PDT
