I'd try editing the pdb to offset the coordinates slightly, then 100
steps of general minimization.
Bill
On 8/9/17 2:21 AM, James Starlight wrote:
> 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
>>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
> _______________________________________________
> 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
Received on Wed Aug 09 2017 - 04:30:02 PDT
