VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Tue Aug 29 2023 - 09:15:58 CDT

Hi,

Can you attach the psf and pdb you generate for a single residue? The
resname in your UREA.pdb (URE) does not match the resname in CGenFF
(UREA), and unless you defined an alias, I'm assuming there were all
sorts of error messages in the terminal when you were running psfgen.

-Josh

On 8/29/23 8:17 AM, Simone Gargano wrote:
> Hi to all,
> I'm trying to use autopsf to generate a psf for a system containing a
> protein surrounded by a solution of water mixed with urea. It all goes
> well except for urea atoms, judged as unparameterized by autopsf. I
> added every Charmm topology file possible, updated to the last
> release, in the correct order. I've managed to go through with the psf
> file generation, but then, when I try to launch NAMD, here is whai i
> get: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE XXX. The
> same problem appears if I use autopsf on the single urea molecole.
>
> This is UREA.pdb (downloaded from
> https://urldefense.com/v3/__https://charmm-gui.org/?doc=archive&lib=csml__;!!DZ3fjg!7x-I5s_jzZ0a0VdVVjiugISWWoWLCIgPk9jPq9Hl_bJVJyGj-riB7CzITzyahJ9ksqMxxw0e2YMcYcvx1qE$
> <https://urldefense.com/v3/__https://charmm-gui.org/?doc=archive&lib=csml__;!!DZ3fjg!5nP2ZOAr0oYnnhu449QPLuNeoaXKsDqxxVgzYs4WBKP9_BY81v-KHVTVItlX-j3zIkJToo8yFxSGid7mtQ$>)
> REMARK   DATE:     2/ 5/21     14:50:16      CREATED BY USER: nathan
> ATOM      1  N1  URE U   1      -1.144  -0.205   0.000  1.00  0.00    
>  UREA
> ATOM      2  H11 URE U   1      -2.036   0.247   0.000  1.00  0.00    
>  UREA
> ATOM      3  H12 URE U   1      -1.088  -1.204  -0.000  1.00  0.00    
>  UREA
> ATOM      4  C2  URE U   1      -0.000   0.543   0.000  1.00  0.00    
>  UREA
> ATOM      5  O2  URE U   1      -0.000   1.782   0.000  1.00  0.00    
>  UREA
> ATOM      6  N3  URE U   1       1.144  -0.205   0.000  1.00  0.00    
>  UREA
> ATOM      7  H31 URE U   1       2.036   0.247  -0.000  1.00  0.00    
>  UREA
> ATOM      8  H32 URE U   1       1.088  -1.204   0.000  1.00  0.00    
>  UREA
> TER       9      UREA    1
> END
>
> While this is the relative section in topology file top_all36_cgenff.rtf
> RESI UREA           0.00  ! CH4N2O, Urea, adm
> GROUP
> ATOM N1    NG2S2   -0.69
> ATOM H11   HGP1     0.34
> ATOM H12   HGP1     0.34
> ATOM C2    CG2O6    0.60
> ATOM O2    OG2D1   -0.58
> ATOM N3    NG2S2   -0.69
> ATOM H31   HGP1     0.34
> ATOM H32   HGP1     0.34
>
> BOND C2 O2  C2 N1  C2 N3
> BOND N1 H11 N1 H12
> BOND N3 H31 N3 H32
> IMPR C2 N1  N3 O2
>
> IC   O2    C2    N1    H11    0.0000    0.00    0.00    0.00 0.0000
> IC   H11   C2    *N1   H12    0.0000    0.00  180.00    0.00 0.0000
> IC   H11   N1    C2    N3     0.0000    0.00  180.00    0.00 0.0000
> IC   N3    N1    *C2   O2     0.0000    0.00  180.00    0.00 0.0000
> IC   N1    C2    N3    H31    0.0000    0.00  180.00    0.00 0.0000
> IC   H31   C2    *N3   H32    0.0000    0.00  180.00    0.00 0.0000
>
> ERROR MESSAGE by VMD
> Warning: I found some undefined atom types in UO1:1 (URE)
> {{0 1 2 3 4 5 6 7} URE UO1 1 {H32 H31 N3 O2 C2 H12 H11 N1}}
> Warning: This molecule contains unparameterized residues. 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io