VMD-L Mailing List

From: Q=C5=CC=C1=CC=CF=D7_=E9=CC=D8=D1?= (mastah_je_at_mail.ru)
Date: Sat Oct 03 2009 - 05:35:24 CDT

Hi, All.
I'm trying to prepare structure, using following:

package require psfgen
topology top_all27_prot_na.rtf #this topfile newest to date
...
segment B {
    pdb 3c.pdb
    last CT2 }
coordpdb 3c.pdb B
guesscoord
writepdb complex.pdb
writepsf complex.psf

in resulting pdb some of prolines are in strange conformation, with bonds between HD1 and N, or HB1 and CG, like this:

ATOM 1219 N PRO A 2 46.419 36.203 0.581 1.00 0.00 B N
ATOM 1220 CD PRO A 2 46.345 37.095 1.750 1.00 0.00 B C
ATOM 1221 HD1 PRO A 2 45.502 36.701 1.137 0.00 0.00 B H
ATOM 1222 HD2 PRO A 2 46.021 37.250 2.805 0.00 0.00 B H
ATOM 1223 CA PRO A 2 47.510 36.598 -0.311 1.00 0.00 B C
ATOM 1224 HA PRO A 2 47.252 36.607 -1.363 0.00 0.00 B H
ATOM 1225 CB PRO A 2 47.968 37.937 0.273 1.00 0.00 B C
ATOM 1226 HB1 PRO A 2 47.327 38.750 -0.137 0.00 0.00 B H
ATOM 1227 HB2 PRO A 2 49.029 38.164 0.044 0.00 0.00 B H
ATOM 1228 CG PRO A 2 46.837 38.375 1.176 1.00 0.00 B C
ATOM 1229 HG1 PRO A 2 46.819 39.469 1.346 0.00 0.00 B H
ATOM 1230 HG2 PRO A 2 45.919 38.748 1.309 0.00 0.00 B H
ATOM 1231 C PRO A 2 48.575 35.525 -0.066 1.00 0.00 B C
ATOM 1232 O PRO A 2 48.616 34.913 0.998 1.00 0.00 B O

Could anybody help me to solve this problem?

Best regards,
Belalov Ilya.