VMD-L Mailing List

From: Simone Gargano (serj9090_at_gmail.com)
Date: Tue Aug 29 2023 - 07:17:49 CDT

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!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.