From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Nov 21 2014 - 10:54:20 CST
Look at the atom type (not name) in the psf file for an atom that is
missing its element field, then search for that type in the MASS lines of
your topology files to see if any of them are missing elements, or are
otherwise inconsistent.
Jim
On Fri, 21 Nov 2014, Francesco Pietra wrote:
> By adding to the .gen file
>
> top_all36_carb.rtf no improvement
>
> top_all22_prot.rtf (which is included in toppar36) some more atoms
> recognized
>
>
> top_all27_prot_na.inp no further help
>
>
> 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 H
> 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 C
> 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
>
> Notice that "grep HG11 *" within toppar36 reveals that such a H-atoms is
> available in
>
> top_all36_cgenff.rtf:ATOM HG11 HGP4 0.400
>
> The same for all other H-atoms here, which were not recognized.
>
> I am trying to use the 36 version as I parameterized the organic ligand
> with that ff.
>
> thanks
> francesco
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Fri, Nov 21, 2014 at 5:06 PM
> Subject: vmd-l: Re: namd-l: problems with in text mode towards pdf and pdb
> files
> To: Jim Phillips <jim_at_ks.uiuc.edu>
> Cc: NAMD <namd-l_at_ks.uiuc.edu>, vmd-l_at_ks.uiuc.edu
>
>
> $ vmd package require psfgen
> Info) VMD for LINUXAMD64, version 1.9.2a20 (March 12, 2013)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) Free system memory: 7037MB (87%)
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: GeForce 6600/PCIe/SSE2
> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Warning) Unable to ascertain filetype from filename 'package'; assuming pdb.
> ERROR) Could not read file package
> ERROR) Loading of startup molecule files aborted.
> /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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