VMD-L Mailing List
From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Dec 11 2015 - 09:25:11 CST
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- Previous message: Josh Vermaas: "Re: namd-l: Problems with GLUP and ASPP with CHARMM36"
- In reply to: Francesco Pietra: "Re: namd-l: Problems with GLUP and ASPP with CHARMM36"
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Ahh, ok. Guesscoord needs to come AFTER the patches. The proton's don't
exist within the program until the patches are applied, and so they
aren't guessed by the first guesscoord.
-Josh
On 12/11/2015 09:21 AM, Francesco Pietra wrote:
> If I understand what you said, in the .gen file, after the statements
> for the components, like
>
> segment PRA {
> last CTER
> pdb parts/PROT_A_segnPRA.pdb
> }
>
> what followed was
>
>
> guesscoord
>
> patch DISU PRA:4 PRA:12
> patch DISU PRA:114 PRA:540
> patch DISU PRA:298 PRA:332
> patch GLUP PRA:235
> patch ASPP PRA:516
>
> regenerate angles dihedrals
>
> writepsf ...
> writepdb ...
> -------------------------------------------
> I was just reexamining the log file for the session with PRA submitted
> deprived of 235 HE2 and 516 HD2: without any warning, it ends with
>
> psfgen) Info: guessing coordinates for 1 atoms (0 non-hydrogen)
> psfgen) applying patch DISU to 2 residues
> psfgen) applying patch DISU to 2 residues
> psfgen) applying patch DISU to 2 residues
> psfgen) applying patch GLUP to 1 residues
> psfgen) applying patch ASPP to 1 residues
> psfgen) regenerating all angles
> psfgen) regenerating all dihedrals
> psfgen) Info: writing psf file .........psf
> psfgen) total of 8558 atoms
> psfgen) total of 8724 bonds
> psfgen) total of 15863 angles
> psfgen) total of 24011 dihedrals
> psfgen) total of 1604 impropers
> psfgen) total of 557 cross-terms
> psfgen) Info: psf file complete.
> psfgen) Info: writing pdb file .....pdb
> psfgen) Info: Atoms with guessed coordinates will have occupancy
> of 0.0.
> psfgen) Info: pdb file complete.
> vmd > PRA:1
> PRA:559
> PRA:4 PRA:12
> PRA:114 PRA:540
> PRA:298 PRA:332
> PRA:235
> PRA:516
> Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> Info) Exiting normally.
>
>
> in the generated pdb the coordinates for 235 and 516 were
>
> ATOM 3533 N GLU A 235 -5.036 21.456 -24.524 1.00
> 0.00 PRA N
> ATOM 3534 HN GLU A 235 -5.104 20.782 -25.276 1.00
> 0.00 PRA H
> ATOM 3535 CA GLU A 235 -3.886 22.387 -24.504 1.00
> 0.00 PRA C
> ATOM 3536 HA GLU A 235 -4.180 23.280 -23.956 1.00
> 0.00 PRA H
> ATOM 3537 CB GLU A 235 -2.711 21.747 -23.755 1.00
> 0.00 PRA C
> ATOM 3538 HB1 GLU A 235 -3.102 21.400 -22.800 1.00
> 0.00 PRA H
> ATOM 3539 HB2 GLU A 235 -2.359 20.864 -24.285 1.00
> 0.00 PRA H
> ATOM 3540 CG GLU A 235 -1.536 22.706 -23.429 1.00
> 0.00 PRA
> ATOM 3541 HG1 GLU A 235 -1.928 23.684 -23.155 1.00
> 0.00 PRA
> ATOM 3542 HG2 GLU A 235 -0.988 22.311 -22.573 1.00
> 0.00 PRA
> ATOM 3543 CD GLU A 235 -0.552 22.867 -24.572 1.00
> 0.00 PRA
> ATOM 3544 OE1 GLU A 235 -0.618 22.089 -25.541 1.00
> 0.00 PRA
> ATOM 3545 OE2 GLU A 235 0.307 23.782 -24.504 1.00
> 0.00 PRA
> ATOM 3546 HE2 GLU A 235 0.000 0.000 0.000 -1.00
> 0.00 PRA
> ATOM 3547 C GLU A 235 -3.417 22.867 -25.892 1.00
> 0.00 PRA C
> ATOM 3548 O GLU A 235 -3.099 24.053 -26.092 1.00
> 0.00 PRA O
>
>
> ATOM 7776 N ASP A 516 -14.861 34.664 -11.875 1.00
> 0.00 PRA N
> ATOM 7777 HN ASP A 516 -14.565 35.279 -11.129 1.00
> 0.00 PRA H
> ATOM 7778 CA ASP A 516 -16.282 34.367 -11.997 1.00
> 0.00 PRA C
> ATOM 7779 HA ASP A 516 -16.503 33.872 -12.944 1.00
> 0.00 PRA H
> ATOM 7780 CB ASP A 516 -16.709 33.460 -10.839 1.00
> 0.00 PRA
> ATOM 7781 HB1 ASP A 516 -16.104 32.553 -10.860 1.00
> 0.00 PRA
> ATOM 7782 HB2 ASP A 516 -16.520 33.955 -9.885 1.00
> 0.00 PRA
> ATOM 7783 CG ASP A 516 -18.170 33.057 -10.903 1.00
> 0.00 PRA
> ATOM 7784 OD1 ASP A 516 -18.895 33.533 -11.792 1.00
> 0.00 PRA
> ATOM 7785 OD2 ASP A 516 -18.593 32.250 -10.047 1.00
> 0.00 PRA
> ATOM 7786 HD2 ASP A 516 0.000 0.000 0.000 -1.00
> 0.00 PRA
> ATOM 7787 C ASP A 516 -16.996 35.708 -11.948 1.00
> 0.00 PRA C
> ATOM 7788 O ASP A 516 -17.054 36.340 -10.898 1.00
> 0.00 PRA O
>
>
> I can't see my mistake, rather I suspect a weird behavior, unless I
> mishandled charmm36, as I uased so far charmm27
>
> francesco
>
> On Fri, Dec 11, 2015 at 3:45 PM, Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
> When did you add in the coordpdb line? Was it above or below this
> section? If atom positions aren't initialized, they will be put at
> the origin by default, which is normally not what people want. My
> guess is that you put it above the section, so that psfgen came
> across atoms it didn't recognize and ignored them, only to have
> you patch them in afterward with the coordinates placed at the origin.
> -Josh Vermaas
>
> On 12/11/2015 05:07 AM, Francesco Pietra wrote:
>> Hello:
>>
>> With CHARMM36, VMD in text mode, the .gen file including:
>>
>> patch GLUP PRA:235
>> patch ASPP PRA:516
>>
>> regenerate angles dihedrals
>>
>> (the protein pdb included all H-atoms), the log file reports that
>> it was unable to read HE2 and HD2 for the above residues. The
>> result was that these atoms were put outside the protein.
>>
>> On removing HE2 and HD2 from the pdb, no more such warnings,
>> however, again, both atoms placed outside the protein. Apparently
>> the patch was accepted.
>> ..............................
>>
>> Moreover, despite the error reported in the log file;
>>
>> psfgen) Toplogy and parameter information for water and ions.
>> psfgen)
>> psfgen) ERROR! FAILED TO RECOGNIZE SET
>> psfgen) ERROR! FAILED TO RECOGNIZE SET
>> psfgen) ERROR! FAILED TO RECOGNIZE IF
>> psfgen) ERROR! FAILED TO RECOGNIZE READ
>> psfgen) Topology for water and ions
>> psfgen)
>> psfgen) ERROR! FAILED TO RECOGNIZE 31
>> psfgen) skipping statements at end of file due to end or return
>> statement
>>
>> a ligand CLA of the protein was set correctly. is there any
>> possible modification of the str file, or should I extract from
>> it the relevant portions in order to skip what VMD is unable to
>> read from CHARMM36?
>> ......................................
>>
>> Grateful for advice
>>
>> francesco pietra
>
>
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- Previous message: Josh Vermaas: "Re: namd-l: Problems with GLUP and ASPP with CHARMM36"
- In reply to: Francesco Pietra: "Re: namd-l: Problems with GLUP and ASPP with CHARMM36"
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