VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 01 2009 - 22:31:52 CDT

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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>