VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Dec 11 2015 - 09:21:34 CST
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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> 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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