From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 21 2014 - 10:06:28 CST
$ vmd package require psfgen
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/usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
/usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
/usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
/usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
/usr/local/lib/vmd/plugins/noarch/tcl /home/francesco/vmd_ORIENT/la1.0
/usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
/usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
/usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
/usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
/usr/local/lib/vmd/plugins/noarch/tcl /home/francesco/vmd_ORIENT/la1.0
/home/francesco/vmd_ORIENT/orient
/home/francesco/vmdplugins /usr/local/lib/vmd/scripts/tcl8.5
/usr/local/lib/vmd/scripts /usr/local/lib/lib
/Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
/usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
/usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
/usr/local/lib/vmd/plugins/noarch/tcl /home/francesco/vmd_ORIENT/la1.0
/home/francesco/vmd_ORIENT/orient
vmd >
As to topoolgies, I tried to add all relevant from charmm36, certainly
nothing lacks for normal proteins, while problems occured with also these.
thanks
francesco
On Fri, Nov 21, 2014 at 4:56 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> As you said, the atoms that psfgen "guessed" coordinates for (because they
> did not have the same name in the input pdb as in the topology file) are
> not having their element field set. This appears to work correctly in my
> simple tests. What does "package require psfgen" return? Are some of
> your topology files missing element names from their "MASS" lines?
>
> Jim
>
>
> On Fri, 21 Nov 2014, Francesco Pietra wrote:
>
> vmd -dispdev text -e filename.gen 2>&1 | tee filename.out
>>
>> the .gen file is organized as follows
>>
>> package require psfgen
>>
>> topology top_all36_cgenff.rtf
>> topology top_all36_lipid.rtf
>> topology top_all36_prot.rtf
>> topology top_water_ions_mod.inp
>> topology top_O2_CGenFF_36.rtf
>> topology LIGAND.rtf
>>
>> segment PRA {
>> last CTER
>> pdb parts/prot_A_segn-PRA.pdb
>> }
>>
>> segment PRB {
>> last CTER
>> pdb parts/prot_B_segn-PRB.pdb
>> }
>>
>>
>> ........................
>> .......................
>> segment WCD {
>> pdb parts/wat_D_segn-WCD.pdb
>> auto none
>> }
>>
>>
>>
>> coordpdb parts/prot_A_segn-PRA.pdb PRA
>> coordpdb parts/prot_B_segn-PRB.pdb PRB
>> coordpdb parts/prot_C_segn-PRC.pdb PRC
>>
>> ............................
>> ..........................
>> guesscoord
>>
>> writepsf xxx.psf
>> writepdb xxx.pdb
>>
>>
>> thanks for advice
>> francesco
>>
>> On Fri, Nov 21, 2014 at 4:29 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>
>>
>>> We're going to need to know what commands you used in VMD to generate
>>> your
>>> output pdb from the input pdb. I assume psfgen was involved somehow.
>>>
>>> Jim
>>>
>>>
>>>
>>> On Fri, 21 Nov 2014, Francesco Pietra wrote:
>>>
>>> Hello:
>>>
>>>> This is to pose two questions:
>>>>
>>>> (1) why certain element symbols are not given by vmd in text mode (ff
>>>> charmm36). As far as I can see, this occurs when the atoms already
>>>> existing
>>>> in the input file are renamed by vmd. For example
>>>>
>>>> INPUT file (from very high resol, so also H-atoms)
>>>> ATOM 1876 N ILE A 121 18.702 56.325 54.575 1.00 9.97
>>>> PRA N
>>>> ATOM 1877 CA ILE A 121 19.542 55.205 54.968 1.00 10.09
>>>> PRA C
>>>> ATOM 1878 C ILE A 121 20.328 54.658 53.776 1.00 9.22
>>>> PRA C
>>>> ATOM 1879 O ILE A 121 19.781 54.584 52.667 1.00 10.52
>>>> PRA O
>>>> ATOM 1880 CB ILE A 121 18.662 54.113 55.632 1.00 11.33
>>>> PRA C
>>>> ATOM 1881 CG1 ILE A 121 19.508 52.942 56.194 1.00 13.73
>>>> PRA C
>>>> ATOM 1882 CG2 ILE A 121 17.478 53.649 54.787 1.00 15.02
>>>> PRA C
>>>> ATOM 1883 CD1 ILE A 121 18.648 52.172 57.211 1.00 17.54
>>>> PRA C
>>>> ATOM 1884 H ILE A 121 18.151 56.223 53.923 1.00 11.97
>>>> PRA H
>>>> ATOM 1885 HA ILE A 121 20.184 55.525 55.636 1.00 12.10
>>>> PRA H
>>>> ATOM 1886 HB ILE A 121 18.264 54.544 56.417 1.00 13.60
>>>> PRA H
>>>> ATOM 1887 HG12 ILE A 121 19.779 52.352 55.473 1.00 16.47
>>>> PRA H
>>>> ATOM 1888 HG13 ILE A 121 20.306 53.285 56.625 1.00 16.47
>>>> PRA H
>>>> ATOM 1889 HG21 ILE A 121 17.003 54.414 54.455 1.00 22.53
>>>> PRA H
>>>> ATOM 1890 HG22 ILE A 121 16.890 53.116 55.325 1.00 22.53
>>>> PRA H
>>>> ATOM 1891 HG23 ILE A 121 17.798 53.126 54.048 1.00 22.53
>>>> PRA H
>>>> ATOM 1892 HD11 ILE A 121 18.385 52.764 57.920 1.00 26.32
>>>> PRA H
>>>> ATOM 1893 HD12 ILE A 121 19.157 51.444 57.574 1.00 26.32
>>>> PRA H
>>>> ATOM 1894 HD13 ILE A 121 17.865 51.829 56.774 1.00 26.32
>>>> PRA H
>>>>
>>>>
>>>> PDB OUTPUT FROM VMD
>>>> ATOM 1904 N ILE A 121 18.702 56.325 54.575 1.00 0.00
>>>> PRA N
>>>> ATOM 1905 HN ILE A 121 18.089 56.129 53.813 0.00 0.00
>>>> PRA
>>>> ATOM 1906 CA ILE A 121 19.542 55.205 54.968 1.00 0.00
>>>> PRA C
>>>> ATOM 1907 HA ILE A 121 20.184 55.525 55.636 1.00 0.00
>>>> PRA H
>>>> ATOM 1908 CB ILE A 121 18.662 54.113 55.632 1.00 0.00
>>>> PRA C
>>>> ATOM 1909 HB ILE A 121 18.264 54.544 56.417 1.00 0.00
>>>> PRA H
>>>> ATOM 1910 CG2 ILE A 121 17.478 53.649 54.787 1.00 0.00
>>>> PRA C
>>>> ATOM 1911 HG21 ILE A 121 17.003 54.414 54.455 1.00 0.00
>>>> PRA H
>>>> ATOM 1912 HG22 ILE A 121 16.890 53.116 55.325 1.00 0.00
>>>> PRA H
>>>> ATOM 1913 HG23 ILE A 121 17.798 53.126 54.048 1.00 0.00
>>>> PRA H
>>>> ATOM 1914 CG1 ILE A 121 19.508 52.942 56.194 1.00 0.00
>>>> PRA C
>>>> ATOM 1915 HG11 ILE A 121 20.182 53.422 56.755 0.00 0.00
>>>> PRA
>>>> ATOM 1916 HG12 ILE A 121 19.779 52.352 55.473 1.00 0.00
>>>> PRA H
>>>> ATOM 1917 CD ILE A 121 18.679 51.833 56.863 0.00 0.00
>>>> PRA
>>>> ATOM 1918 HD1 ILE A 121 19.348 51.057 57.293 0.00 0.00
>>>> PRA
>>>> ATOM 1919 HD2 ILE A 121 18.057 52.250 57.684 0.00 0.00
>>>> PRA
>>>> ATOM 1920 HD3 ILE A 121 18.008 51.339 56.129 0.00 0.00
>>>> PRA
>>>> ATOM 1921 C ILE A 121 20.328 54.658 53.776 1.00 0.00
>>>> PRA C
>>>> ATOM 1922 O ILE A 121 19.781 54.584 52.667 1.00 0.00
>>>> PRA O
>>>>
>>>>
>>>>
>>>> (2) Could the lack of atom symbols in the pdb associated to the psf
>>>> file,
>>>> as above, pose problems in using such files for molecular dynamics? As
>>>> also
>>>> MD might be involved, I am also posting ti NAMD
>>>>
>>>> thanks
>>>> francesco pietra
>>>>
>>>>
>>>>
>>
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