VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Sep 18 2008 - 10:13:55 CDT

Hi Rudra,

Please take a look at your file again. Peter is right. For example, if
you look at the first lines of your file, you have this:

#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 #7 has a three-letter identifier (NR2), which makes the
coordinates move one space forward.

Cheers,
Michel

On Thu, Sep 18, 2008 at 4:34 PM, Rudra Banerjee <bnrj.rudra_at_yahoo.com> wrote:
> the extra decimal points (i dont know how n why) comes when i copy the file in the mail...its not present in the original pdb file.
> guess the problem is with the naming....let me check and i ll tell (or bother) you
> regards
>
>
> --
> Rudra
> JRF; SNBNCBS
> http://www.bose.res.in/~rudra
>
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>
> ----- Original Message ----
> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
> To: Rudra Banerjee <bnrj.rudra_at_yahoo.com>
> Cc: vmd-l_at_ks.uiuc.edu
> Sent: Thursday, 18 September, 2008 5:48:15 PM
> Subject: Re: vmd-l: psfgen problem
>
> 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?
>>
>>
>>
>>
>
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