VMD-L Mailing List

From: Jernej Zidar (jernej.zidar_at_gmail.com)
Date: Thu Aug 11 2011 - 01:41:08 CDT

A word of advice also:
Try always to use a pair of PSF and PDB files. In some peculiar cases
VMD gets the connectivity data wrong unless the PSF file is present as
well.

Regards,
Jernej

On Thu, Aug 11, 2011 at 13:14, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Thu, Aug 11, 2011 at 12:10 AM, Marc Charendoff
> <mcharend_at_sbcglobal.net> wrote:
>> Hello,
>>     I am trying to create the hydrolysis product of a lactone ring in
>> Molefacture from an existing structure so as to show the resulting alcohol
>> and carboxylate functional groups. Everything looks ok in Molefacture, but
>> when I write the resulting pdb file and reopen it in VMD I still see that
>> the old carbonyl carbon to ether oxygen linkage remains. What am I missing?
>
> a pdb file (as written by VMD) contains no information about bonding
> and this is recovered heuristically from atom radii and distances on
> loading the file.  if you save a .pdb _and_ .psf file and then load the
> .psf file with the .pdb file, then the bonding pattern will be read from
> the psf. file rather than guessed heuristically.
>
> there are also some other file formats that store bond information
> alongside the coordinate information.
>
> axel.
>
>> Any guidance anyone could provide would be greatly appreciated. My current
>> (failed structure) is below:
>> REMARK original generated coordinate pdb file
>> HETATM    1  OAO UNK B 253      29.310  34.583  39.046  1.00  0.00      MOL
>>  O
>> HETATM    2  CAN UNK B 253      28.739  33.746  38.365  1.00  0.00      MOL
>>  C
>> HETATM    3  OAR UNK B 253      28.383  33.934  37.053  1.00  0.00      MOL
>>  O
>> HETATM    4  CAP UNK B 253      29.367  32.494  36.772  1.00  0.00      MOL
>>  C
>> HETATM    5  CAQ UNK B 253      28.673  31.448  37.720  1.00  0.00      MOL
>>  C
>> HETATM    6  CAM UNK B 253      28.249  32.381  38.825  1.00  0.00      MOL
>>  C
>> HETATM    7  NAK UNK B 253      27.290  32.448  39.923  1.00  0.00      MOL
>>  N
>> HETATM    8  HA2 UNK B 253      26.388  32.836  39.732  1.00  0.00      MOL
>>  H
>> HETATM    9  CAJ UNK B 253      27.531  32.036  41.135  1.00  0.00      MOL
>>  C
>> HETATM   10  OAL UNK B 253      28.345  31.134  41.344  1.00  0.00      MOL
>>  O
>> HETATM   11  CAI UNK B 253      26.766  32.648  42.312  1.00  0.00      MOL
>>  C
>> HETATM   12  CAH UNK B 253      25.626  33.644  42.084  1.00  0.00      MOL
>>  C
>> HETATM   13  CAG UNK B 253      25.773  35.117  41.669  1.00  0.00      MOL
>>  C
>> HETATM   14  CAF UNK B 253      24.963  36.102  42.502  1.00  0.00      MOL
>>  C
>> HETATM   15  CAE UNK B 253      25.869  36.510  43.652  1.00  0.00      MOL
>>  C
>> HETATM   16  CAD UNK B 253      25.128  37.706  44.254  1.00  0.00      MOL
>>  C
>> HETATM   17  CAC UNK B 253      24.353  37.255  45.496  1.00  0.00      MOL
>>  C
>> HETATM   18  CAB UNK B 253      25.083  36.081  46.154  1.00  0.00      MOL
>>  C
>> HETATM   19  CAA UNK B 253      24.070  35.189  46.874  1.00  0.00      MOL
>>  C
>> HETATM   20  CAS UNK B 253      23.084  34.560  45.886  1.00  0.00      MOL
>>  C
>> HETATM   21  CAT UNK B 253      23.849  33.685  44.890  1.00  0.00      MOL
>>  C
>> HETATM   22  OAM UNK B 253      29.738  32.082  35.940  1.00  0.00      MOL
>>  O
>> END
>> The desired product (w/regards to the opened lactone ring) is as follows:
>>
>> HETATM 2104  O4  C6L A 253     -15.207  -7.751  15.430  0.90 20.62
>> O
>>
>> HETATM 2105  C5  C6L A 253     -16.064  -6.960  15.205  0.90 21.63
>> C
>>
>> HETATM 2106  C6  C6L A 253     -16.833  -6.344  16.384  0.90 24.08
>> C
>>
>> HETATM 2107  C7  C6L A 253     -17.971  -5.350  16.157  0.90 29.16
>> C
>>
>> HETATM 2108  C8  C6L A 253     -17.824  -3.877  15.742  0.90 31.82
>> C
>>
>> HETATM 2109  C9  C6L A 253     -18.634  -2.892  16.575  0.90 30.57
>> C
>>
>> HETATM 2110  C10 C6L A 253     -17.724  -2.483  17.730  0.90 30.72
>> C
>>
>> HETATM 2111  N1  C6L A 253     -16.307  -6.546  13.996  0.90 21.59
>> N
>>
>> HETATM 2112  C3  C6L A 253     -15.573  -6.989  12.814  0.90 21.15
>> C
>>
>> HETATM 2113  C4  C6L A 253     -14.550  -5.958  12.306  0.90 21.16
>> C
>>
>> HETATM 2114  O2  C6L A 253     -14.258  -5.884  11.135  0.90 19.59
>> O
>>
>> HETATM 2115  O1  C6L A 253     -13.945  -5.227  13.080  0.90 17.44
>> O
>>
>> HETATM 2116  C2  C6L A 253     -16.571  -7.274  11.693  0.90 22.47
>> C
>>
>> HETATM 2117  C1  C6L A 253     -16.106  -8.309  10.659  0.90 22.14
>> C
>>
>> HETATM 2118  O3  C6L A 253     -15.111  -7.792   9.768  0.90 20.66
>> O
>>
>> END
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
> 

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