VMD-L Mailing List

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Sat May 02 2009 - 14:17:25 CDT

Hi Peter,
yes, I found the MG residue and it does "just work", as advertised :).
My GTP topology file made from GUA and ATP looks working as well. So no
further questions for now.
Thank you for your help

Sasha

Peter Freddolino wrote:
> Hi Sasha,
> most of the charmm topology files have an MG residue for Mg2+... if you
> have your residue named properly, it should Just Work (tm).
> Peter
>
> Sasha Buzko wrote:
>
>> Hi Peter,
>> thanks for your help. The ATP case now works with the capitalization of
>> "end", as you suggested.
>> With that, I'll move on to the actual goal (protein/GTP/Mg). I saw an
>> earlier post about GTP, and will try the combination of GUA and ATP
>> records.
>> As for the coordinated Mg2+ ion, could you possibly suggest a reasonable
>> way to proceed here with autopsf? I haven't seen any metal parameters,
>> and any hints would be very helpful.
>>
>> Thanks again
>>
>> Sasha
>>
>>
>> Peter Freddolino wrote:
>>
>>> Hi Sasha,
>>> I see what's going on... top_all27_na.rtf has an "end" rather than "END"
>>> at the end of the file, which is unusual and not properly recognized by
>>> autopsf. I'll fix autopsf for the future; for now things should work
>>> fine if you change the "end" at the end of that file to "END".
>>> Thanks for working through this.
>>> Best,
>>> Peter
>>>
>>> Sasha Buzko wrote:
>>>
>>>
>>>> Peter,
>>>> same thing, just with the top files..
>>>>
>>>> I narrowed the problem down all to way to ATP itself (cut out of the pdb
>>>> file, below in the message). It generates the error message with unknown
>>>> ATP residue when using top_all27_na.rtf and top_all27_na_nad_ppi.str in
>>>> the Topology box..
>>>>
>>>> Thanks
>>>>
>>>> Sasha
>>>>
>>>>
>>>> HETATM 3612 PG ATP A 1 10.853 19.115 59.704 1.00
>>>> 0.00 P
>>>> HETATM 3613 O1G ATP A 1 10.091 17.895 59.212 1.00
>>>> 0.00 O
>>>> HETATM 3614 O2G ATP A 1 11.605 19.862 58.626 1.00
>>>> 0.00 O
>>>> HETATM 3615 O3G ATP A 1 10.076 20.017 60.630 1.00
>>>> 0.00 O
>>>> HETATM 3616 PB ATP A 1 13.437 17.690 60.353 1.00
>>>> 0.00 P
>>>> HETATM 3617 O1B ATP A 1 13.048 16.248 60.524 1.00
>>>> 0.00 O
>>>> HETATM 3618 O2B ATP A 1 14.622 18.005 61.154 1.00
>>>> 0.00 O
>>>> HETATM 3619 O3B ATP A 1 12.069 18.463 60.701 1.00
>>>> 0.00 O
>>>> HETATM 3620 PA ATP A 1 14.454 18.753 57.580 1.00
>>>> 0.00 P
>>>> HETATM 3621 O1A ATP A 1 13.686 18.469 56.304 1.00
>>>> 0.00 O
>>>> HETATM 3622 O2A ATP A 1 14.374 20.189 58.045 1.00
>>>> 0.00 O
>>>> HETATM 3623 O3A ATP A 1 13.999 17.746 58.768 1.00
>>>> 0.00 O
>>>> HETATM 3624 O5' ATP A 1 15.974 18.283 57.437 1.00
>>>> 0.00 O
>>>> HETATM 3625 C5' ATP A 1 16.690 18.559 58.640 1.00
>>>> 0.00 C
>>>> HETATM 3626 C4' ATP A 1 18.073 17.916 58.517 1.00
>>>> 0.00 C
>>>> HETATM 3627 O4' ATP A 1 18.860 18.855 57.821 1.00
>>>> 0.00 O
>>>> HETATM 3628 C3' ATP A 1 18.857 17.816 59.772 1.00
>>>> 0.00 C
>>>> HETATM 3629 O3' ATP A 1 19.943 16.977 59.448 1.00
>>>> 0.00 O
>>>> HETATM 3630 C2' ATP A 1 19.465 19.223 59.926 1.00
>>>> 0.00 C
>>>> HETATM 3631 O2' ATP A 1 20.706 19.285 60.577 1.00
>>>> 0.00 O
>>>> HETATM 3632 C1' ATP A 1 19.732 19.701 58.553 1.00
>>>> 0.00 C
>>>> HETATM 3633 N9 ATP A 1 19.629 21.190 58.334 1.00
>>>> 0.00 N
>>>> HETATM 3634 C8 ATP A 1 18.484 21.885 58.172 1.00
>>>> 0.00 C
>>>> HETATM 3635 N7 ATP A 1 18.729 23.180 58.001 1.00
>>>> 0.00 N
>>>> HETATM 3636 C5 ATP A 1 20.060 23.306 58.052 1.00
>>>> 0.00 C
>>>> HETATM 3637 C6 ATP A 1 20.838 24.498 57.927 1.00
>>>> 0.00 C
>>>> HETATM 3638 N6 ATP A 1 20.204 25.689 57.721 1.00
>>>> 0.00 N
>>>> HETATM 3639 N1 ATP A 1 22.211 24.411 58.013 1.00
>>>> 0.00 N
>>>> HETATM 3640 C2 ATP A 1 22.724 23.167 58.224 1.00
>>>> 0.00 C
>>>> HETATM 3641 N3 ATP A 1 21.997 22.042 58.350 1.00
>>>> 0.00 N
>>>> HETATM 3642 C4 ATP A 1 20.647 22.066 58.273 1.00
>>>> 0.00 C
>>>> CONECT 3612 3613 3613 3614 3615 3619
>>>> CONECT 3613 3612 3612
>>>> CONECT 3614 3612
>>>> CONECT 3615 3612
>>>> CONECT 3616 3617 3617 3618 3619 3623
>>>> CONECT 3617 3616 3616
>>>> CONECT 3618 3616
>>>> CONECT 3619 3612 3616
>>>> CONECT 3620 3621 3621 3622 3623 3624
>>>> CONECT 3621 3620 3620
>>>> CONECT 3622 3620
>>>> CONECT 3623 3616 3620
>>>> CONECT 3624 3620 3625
>>>> CONECT 3625 3624 3626
>>>> CONECT 3626 3625 3627 3628
>>>> CONECT 3627 3626 3632
>>>> CONECT 3628 3626 3629 3630
>>>> CONECT 3629 3628
>>>> CONECT 3630 3628 3631 3632
>>>> CONECT 3631 3630
>>>> CONECT 3632 3627 3630 3633
>>>> CONECT 3633 3632 3634 3642
>>>> CONECT 3634 3633 3635 3635
>>>> CONECT 3635 3634 3634 3636
>>>> CONECT 3636 3635 3637 3642 3642
>>>> CONECT 3637 3636 3638 3639 3639
>>>> CONECT 3638 3637
>>>> CONECT 3639 3637 3637 3640
>>>> CONECT 3640 3639 3641 3641
>>>> CONECT 3641 3640 3640 3642
>>>> CONECT 3642 3633 3636 3636 3641
>>>> END
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Peter Freddolino wrote:
>>>>
>>>>
>>>>> Please try without including the par_ file, which is a parameter file
>>>>> and probably gave errors when you tried to read it. I should have noted
>>>>> that explicitly; in charmm one would load both the topology and
>>>>> parameter files, but for psfgen/autopsf you only want the topology file.
>>>>> Peter
>>>>>
>>>>> Sasha Buzko wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Thank you, Peter.
>>>>>> Surprisingly enough, I now get "unknown residue type ATP".
>>>>>>
>>>>>> The files added in the Topology box:
>>>>>> top_all27_prot_lipid.inp
>>>>>> top_all27_na.rtf
>>>>>> par_all27_na.prm
>>>>>> toppar_all27_na_nad_ppi.str
>>>>>>
>>>>>> The source PDB residue/atom naming is still consistent with the
>>>>>> parameter files.. The first file (top_all27_prot_lipid.inp) wasn't part
>>>>>> of the bundled distribution, but came from another site. It worked fine
>>>>>> on kinase alone, though..
>>>>>>
>>>>>> Sasha
>>>>>>
>>>>>>
>>>>>> Peter Freddolino wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Sasha,
>>>>>>> as noted in the comments at the top of the stream file that you are
>>>>>>> including, you also need to read top_all27_na.rtf in order yo use that
>>>>>>> stream file.
>>>>>>> Peter
>>>>>>>
>>>>>>> Sasha Buzko wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> I'm trying to use NAMD to run MD of a protein with bound GTP and a
>>>>>>>> magnesium ion, in order to compare to my prior Amber simulations. But
>>>>>>>> since the GTP/Mg setup has so far failed miserably, I'm taking smaller
>>>>>>>> steps. So at this point, it's a protein kinase with ATP bound.
>>>>>>>>
>>>>>>>> When running GUI of autopfs with the protein-ATP complex, chain
>>>>>>>> generation fails ("failed at end of segment"). Tk console shows the
>>>>>>>> error as "unknown atom type ON3". It refers to one of the phosphate
>>>>>>>> oxygens in the ATP, according to the toppar file.
>>>>>>>>
>>>>>>>> I'm using VMD 1.8.6 and top_all27_prot_lipid.inp. As the source of the
>>>>>>>> ATP parameters, I'm loading toppar_all27_na_nad_ppi.str from the
>>>>>>>> toppar_c35b2_c36a2 distribution. I checked atom/residue naming between
>>>>>>>> the parameter file and the PDB source, and they are identical.
>>>>>>>>
>>>>>>>> Could anyone suggest a possible source of this error?
>>>>>>>>
>>>>>>>> Thanks in advance for any suggestions
>>>>>>>>
>>>>>>>> Sasha
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>
>