VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 18 2008 - 07:18:15 CDT

Hi Rudra,
the atom names in the pdb need to match up with the names (second
column) in the topology entry, not the types (third column).
Also, if you look at your pdb file you'll note that you still have some
extra decimal points and other places where the columns aren't properly
aligned.
Peter

Rudra Banerjee wrote:
> hello friends,
> plz forgive me for resending the same file. actually the molecule structure was craped due to the missing tab formating . so i am resending it with corrected structure
> i am trying to generate osf file for acridine orange with the initial coordinate file:
>
> #CRYST1 0.000 0..000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 CA MAC A 1 -3.039 1.934 -0.283 1.00 0.00 C
> ATOM 2 CA MAC A 1 -3.189 0.892 0.625 1.00 0.00 C
> ATOM 3 CA MAC A 1 -2.112 0.042 0.894 1.00 0.00 C
> ATOM 4 CA MAC A 1 -0.879 0.204 0.276 1.00 0.00 C
> ATOM 5 CA MAC A 1 -0.733 1.261 -0.643 1.00 0.00 C
> ATOM 6 CA MAC A 1 -1.812 2.120 -0.917 1.00 0.00 C
> ATOM 7 NR2 MAC A 1 0.123 -0.642 0.571 1.00 0.00 N
> ATOM 8 CA MAC A 1 1.315 -0.482 -0.029 1.00 0.00 C
> ATOM 9 CA MAC A 1 1.562 0.544 -0.962 1.00 0.00 C
> ATOM 10 CA MAC A 1 0.512 1..419 -1.262 1.00 0.00 C
> ATOM 11 CA MAC A 1 2.353 -1.354 0.273 1.00 0.00 C
> ATOM 12 CA MAC A 1 3.613 -1.234 -0.321 1.00 0.00 C
> ATOM 13 CA MAC A 1 3.854 -0.212 -1.232 1.00 0.00 C
> ATOM 14 CA MAC A 1 2.827 0.670 -1.563 1.00 0.00 C
> ATOM 15 NH2 MAC A 1 4.671 -2.189 0.006 1.00 0.00 N
> ATOM 16 NH2 MAC A 1 -4.299 0.713 1.207 1.00 0.00 N
> ATOM 17 HP MAC A 1 -3.879 2.612 -0.492 1.00 0.00 H
> ATOM 18 HP MAC A 1 -2.248 -0.784 1.607 1.00 0.00 H
> ATOM 19 HP MAC A 1 -1.685 2.949 -1.629 1.00 0..00 H
> ATOM 20 HP MAC A 1 0.669 2.239 -1.978 1..00 0.00 H
> ATOM 21 HP MAC A 1 2.175 -2.167 0.992 1.00 0.00 H
> ATOM 22 HP MAC A 1 4.846 -0.106 -1.696 1.00 0.00 H
> ATOM 23 HP MAC A 1 3.013 1.474 -2.290 1.00 0.00 H
> ATOM 24 CA MAC A 1 5.628 -2.116 -0.419 1.00 0.00 C
> ATOM 25 CA MAC A 1 -5.107 1.352 1.005 1.00 0.00 C
> ATOM 26 CA MAC A 1 -4.392 -0.073 1.897 1.00 0.00 C
> ATOM 27 HP MAC A 1 6.081 -1.136 -0.148 1.00 0.00 H
> ATOM 28 HP MAC A 1 5.550 -2.185 -1.527 1.00 0.00 H
> ATOM 29 HP MAC A 1 6.270 -2.939 -0.032 1.00 0.00 H
> ATOM 30 HP MAC A 1 -4.830 2.397 1.270 1.00 0.00 H
> ATOM 31 HP MAC A 1 -5.986 1.045 1.614 1.00 0.00 H
> ATOM 32 HP MAC A 1 -5.354 1.307 -0.080 1.00 0.00 H
> ATOM 33 HP MAC A 1 -5.425 -0.085 2.310 1.00 0.00 H
> ATOM 34 HP MAC A 1 -4.187 -1.041 1.386 1.00 0.00 H
> ATOM 35 HP MAC A 1 -3.663 0..071 2.725 1.00 0.00 H
> ATOM 36 CA MAC A 1 4.407 -3.273 0.925 1.00 0.00 C
> ATOM 37 HP MAC A 1 3.586 -3.909 0.524 1.00 0.00 H
> ATOM 38 HP MAC A 1 5.323 -3.895 1.040 1.00 0.00 H
> ATOM 39 HP MAC A 1 4.096 -2.858 1.910 1.00 0.00 H
> END
> and since it is not supplied in charmm force field, i have generated one for this..the corresponding part looks like:
> !MY RESIDUE
>
> RESI MAC 0.00
> GROUP
> ATOM N2 NH2 -0.47 !
> ATOM HA1 HB 0.31 !
> ATOM CA CA 0.07 !
> ATOM HA2 HB 0.09 !
> ATOM HA3 HB 0.00 !
> GROUP !
> ATOM CB CA -0.18 !
> ATOM HB1 HB 0.09 !
> ATOM HB2 HB 0.09 !
> ATOM HB3 HB 0.00 !
> GROUP !
> ATOM CD1 CA -0.115 !
> ATOM HD1 HP 0.115 !
> GROUP !
> ATOM CE1 CA -0.115 !
> ATOM HE1 HP 0.115 ! HE1 H1 H4
> GROUP ! | | |
> ATOM CZ CA 0.00 ! HA2 HD1 CE1 C1 C4 H5 H83
> GROUP ! | \ // \ / \\ / \\ / |
> ATOM CG CA 0.00 ! HA1-CA CD1 CZ C2 C5 --C8-H82
> GROUP ! | | || | | \
> ATOM CD2 CA -0.115 ! HA3 N2-- CG CE2 C3 C6-N1 H81
> ATOM HD2 HP 0.115 ! | \\ / \ // \ // |
> GROUP ! HB1-CB-HB3 CD2 N C7 C9-H93
> ATOM CE2 CA 0.47 ! | | / / \
> ATOM N NR3 -0.47 ! HB2 HD2 H7 H91 H92
> GROUP !
> ATOM C1 CA -0.115 !
> ATOM H1 HP 0.115 !
> GROUP !
> ATOM C2 CA 0.00 !
> ATOM C3 CA 0.00 !
> GROUP !
> ATOM C4 CA -0.115 !
> ATOM H4 HP 0.115 !
> GROUP !
> ATOM C5 CA -0.115 !
> ATOM H5 HP 0.115 !
> GROUP !
> ATOM C7 CA -0.115 !
> ATOM H7 HP 0.115 !
> GROUP !
> ATOM C6 CA 0.07 !
> ATOM N1 NH2 -0.047 !
> ATOM C8 CA 0.08 !
> ATOM C9 CA 0.08 !
> ATOM H81 HB 0.04 !
> ATOM H82 HB 0.04 !
> ATOM H83 HB 0.04 !
> ATOM H91 HB 0.04 !
> ATOM H92 HB 0.04 !
> ATOM H93 HB 0.04 !
> BOND CG CD1 CE1 CZ CZ C1 C2 C3 CE2 CD2 CE2 N C2 C4 C5 C6
> BOND N2 CA CA HA1 CA HA2 CA HA3 N CB CB HB1 CB HB2 CB HB3
> BOND CD1 HD1 CE1 HE1 C1 H1 C4 H4 C5 H5 C7 H7 CD2 HD2
> BOND N1 C8 N1 C9 C9 H91 C9 H92 C9 H93 C8 H81 C8 H82 C8 H83
> DOUBLE CD1 CE1 CG CD2 CZ CE2 C1 C2 C3 N C4 C5 C6 C7
> IMPR N C CA HN C CA
> DONOR N N1 N2
> ACCEPTOR CA CB CE2 C3 C8 C9
>
> IC s are not given as i have supplied all the coordinates in the pdb file. but it is not of much help.
> can you people suggest me where i am going wrong?
>
>
>
>