From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Dec 13 2015 - 15:59:37 CST
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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