[gmx-users] Problem with amidation in pdb2gmx

[Mitchell Stanton-Cook]

Yeah. I select none for the terminal residues.

Gromacs was compiled by myself. I have used this version in production 
runs for the last 5 months.

Cheers

Mitch

Justin A. Lemkul wrote:
> Sorry, clicked 'send' too soon.  How was this version of Gromacs compiled?  I
> remember submitting a bugzilla not too long ago about a similar problem, and it
> ended up being that the Ubuntu package was broken.  Re-compiling from source
> fixed the problem.  The -ter response was a knee-jerk reaction, as a related
> problem is somewhere in the list archive.
>
> -Justin
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>   
>> Quoting s4026869 at student.uq.edu.au:
>>
>>     
>>> Hello all,
>>>
>>> I have a protein with missing N- and C- terminus residues. I am
>>> simulating a complex. To avoid in-silico charge interactions at the
>>> wrong places due to the missing residues I have performed acetylation
>>> and amidation.
>>>
>>>
>>> When running pdb2gmx (GMX331) I experience a problem -
>>>
>>>
>>> pdb2gmx -f blah.pdb -o blah.gro -p blah.top -water spc -ter -ignh -merge
>>>       
>> Are you choosing 'none' for your termini?
>>
>> -Justin
>>
>>     
>>> Fatal error:
>>> Atom H not found in residue 177 while adding improper
>>>
>>>
>>> 177 is the number of the NH2 cap after re-numbering of the pdb file.
>>>
>>>
>>> EXTRACT FROM THE PDB FILE -
>>>
>>> .....
>>> ATOM   1382  N   NH2 A 181      15.061  41.575  44.283  0.00  0.00
>>> N
>>> ATOM   1383  H1  NH2 A 181      14.812  41.813  45.232  0.00  0.00
>>> H
>>> ATOM   1384  H2  NH2 A 181      16.038  41.447  44.027  0.00  0.00
>>> H
>>> ....
>>>
>>>
>>> The ffG53a6.rtp has the NH2 as -
>>>
>>>
>>> [ NH2 ]
>>>   [ atoms ]
>>>       N    NT   -0.83    0
>>>       H1    H   0.415    0
>>>       H2    H   0.415    0
>>>   [ bonds ]
>>>        N    H1  gb_2
>>>        N    H2  gb_2
>>>       -C    N   gb_9
>>>   [ angles ]
>>>       -O -C N  ga_33
>>>       -CA -C N ga_19
>>>       -C N H1  ga_23
>>>       -C N H2  ga_23
>>>       H1 N H2  ga_24
>>>   [ dihedrals ]
>>>      -CA -C N H1 gd_14
>>>   [ impropers ]
>>>      -C -O N -CA gi_1
>>>       N  H H  -C gi_1
>>>
>>>
>>> Am I missing something?
>>>
>>> I reproduce this error with GMX332.
>>>
>>> However, if I use pdb2gmx with v3.2.1, pdb2gmx does not complain !
>>>
>>>
>>> Does anyone have any ideas/fixes?
>>>
>>>
>>> Cheers
>>>
>>> Mitch
>>>
>>>
>>>
>>> _______________________________________________
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>>>       
>>
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul at vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> ========================================
>> _______________________________________________
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>>     
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
> _______________________________________________
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