VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Dec 14 2015 - 09:04:21 CST

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
>>>>>
>>>>>
>>>>>
>>>>
>>>
>