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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Dec 14 2015 - 14:52:18 CST

I had seen Victor' post, not Jim's post when I lastly posted. Again, if
relevant, my pdb file in /parts of the .gen file had all protons (as I
wrote before) and also a complete element column:

ATOM 1 N GLU A 1 -37.150 25.869 -38.254 1.00 0.00
PRA N
ATOM 2 HT1 GLU A 1 -36.791 25.374 -37.450 1.00 0.00
PRA H
ATOM 3 HT2 GLU A 1 -38.160 25.847 -38.243 1.00 0.00
PRA H
ATOM 4 HT3 GLU A 1 -36.845 26.831 -38.227 1.00 0.00
PRA H

Also all other pdb files , for the protein ligands, had a complete element
column.

francesco

On Mon, Dec 14, 2015 at 4:04 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> OK, then that's why psfgen isn't writing elements to the pdb file. Since
> masses are available psfgen could guess elements pretty well. Any
> suggestions from the list?
>
> Also, anybody know what "AUTOGENERATE ANGLES DIHEDRALS PATCH" is supposed
> to mean in top_all36_na.rtf? (Specifically, what does "PATCH" indicate?)
>
>
> Jim
>
>
> On Sun, 13 Dec 2015, Francesco Pietra wrote:
>
> Contrary to charmm27, charmm36 rtf have no element
>>
>>
>> charmm27
>> MASS 1 H 1.00800 H ! polar H
>> MASS 2 HC 1.00800 H ! N-ter H
>> MASS 3 HA 1.00800 H ! nonpolar H
>> MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
>> MASS 5 HP 1.00800 H ! aromatic H
>> MASS 6 HB 1.00800 H ! backbone H
>>
>> charmm36
>> MASS 31 H 1.00800 ! polar H
>> MASS 32 HC 1.00800 ! N-ter H
>> MASS 33 HA 1.00800 ! nonpolar H
>> MASS 34 HP 1.00800 ! aromatic H
>> MASS 35 HB1 1.00800 ! backbone H
>> MASS 36 HB2 1.00800 ! aliphatic backbone H, to CT2
>>
>> if this is what you want
>>
>> francesco
>>
>> On Sun, Dec 13, 2015 at 9:32 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>
>>
>>> 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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