From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 21 2014 - 09:39:56 CST
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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