Re: vmd-l: Re: VMD-NAMD and PDB element column

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun Dec 13 2015 - 14:32:38 CST

If you "grep -i mass" your topology files are there lines that lack the
element field?

Jim

On Sun, 13 Dec 2015, Francesco Pietra wrote:

> The initial pdb file for the protein came from the H++server, thus
> protonated and in AMBER format. The psfgen, with all the needed aliases,
> was set for TIP4P water (Freddolino kit). The toppar for water_ions set CLA
> in correctly, while for parameters I had to extract the relevant portion
> for CLA. Toppar heme was only used for dioxygen
>
>
> package require psfgen
>
> topology top_all36_prot.rtf
> topology myion.rtf
> topology toppar_water_ions.str
> topology toppar_all36_prot_heme_O2-mod.str
> topology tip4p.top
>
> pdbalias atom ALA H HN
> pdbalias atom ARG H HN
> pdbalias atom ARG HB2 HB1
> pdbalias atom ARG HB3 HB2
> pdbalias atom ARG HG2 HG1
>
>
> francesco
>
>
>
>
> On Sun, Dec 13, 2015 at 7:17 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
>>
>> I suspect that the corresponding MASS lines in your topology file are
>> missing the element field, so an empty string over-writes the element field
>> which the patch is applied. A different topology file that contains
>> elements was apparently used to build the initial structure.
>>
>> How exactly did you produce this file?
>>
>> Jim
>>
>>
>> On Sat, 12 Dec 2015, Francesco Pietra wrote:
>>
>> Hello:
>>> As far as I can remember, NAMD does not read the element column in the pdb
>>> file prepared with psfgen.
>>>
>>> Even if true, why VMD (1.9.2 Linux in text mode) does not fully build the
>>> element column of CYS CYSD patched
>>> ATOM 7589 C HSD A 502 -9.956 31.185 -18.889 1.00 0.00
>>> PRA C
>>> ATOM 7590 O HSD A 502 -10.454 31.249 -20.013 1.00 0.00
>>> PRA O
>>> ATOM 7591 N CYS A 503 -8.702 30.797 -18.663 1.00 0.00
>>> PRA N
>>> ATOM 7592 HN CYS A 503 -8.361 30.759 -17.713 1.00 0.00
>>> PRA H
>>> ATOM 7593 CA CYS A 503 -7.905 30.157 -19.699 1.00 0.00
>>> PRA C
>>> ATOM 7594 HA CYS A 503 -7.913 30.790 -20.584 1.00 0.00
>>> PRA H
>>> ATOM 7595 CB CYS A 503 -6.462 29.977 -19.236 1.00 0.00
>>> PRA
>>> ATOM 7596 HB1 CYS A 503 -6.017 30.961 -19.091 1.00 0.00
>>> PRA
>>> ATOM 7597 HB2 CYS A 503 -6.440 29.431 -18.291 1.00 0.00
>>> PRA
>>> ATOM 7598 SG CYS A 503 -5.529 29.081 -20.452 1.00 0.00
>>> PRA
>>> ATOM 7599 C CYS A 503 -8.506 28.785 -19.988 1.00 0.00
>>> PRA C
>>> ATOM 7600 O CYS A 503 -8.925 28.083 -19.061 1.00 0.00
>>> PRA O
>>>
>>> and CYM
>>>
>>> ATOM 46 N CYM A 4 -36.415 29.381 -46.642 1.00 0.00
>>> PRA N
>>> ATOM 47 HN CYM A 4 -35.975 29.520 -45.744 1.00 0.00
>>> PRA H
>>> ATOM 48 CA CYM A 4 -35.816 29.990 -47.828 1.00 0.00
>>> PRA C
>>> ATOM 49 HA CYM A 4 -36.195 29.506 -48.728 1.00 0.00
>>> PRA H
>>> ATOM 50 CB CYM A 4 -36.182 31.474 -47.915 1.00 0.00
>>> PRA
>>> ATOM 51 HB1 CYM A 4 -35.625 31.955 -48.719 1.00 0.00
>>> PRA H
>>> ATOM 52 HB2 CYM A 4 -37.242 31.549 -48.160 1.00 0.00
>>> PRA H
>>> ATOM 53 SG CYM A 4 -35.921 32.354 -46.370 1.00 0.00
>>> PRA
>>> ATOM 54 C CYM A 4 -34.294 29.804 -47.881 1.00 0.00
>>> PRA C
>>> ATOM 55 O CYM A 4 -33.602 30.512 -48.604 1.00 0.00
>>> PRA O
>>>
>>> (which are graphically perfectly built)?
>>>
>>> francesco pietra
>>>
>>>
>>
>

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