VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Dec 03 2009 - 05:31:58 CST

Dear Francesco,

cgsolvate is, in fact, completely obsolete because the official solvate
tool now lets you use whatever solvent you want (see the documentation
for details) -- it was always a hack, and the current solution is
cleaner and more versatile. You should just be able to feed solvate the
equilibrated CG water box that comes with cgsolvate as a nonstandard
solvent.

Best,
Peter

Francesco Pietra wrote:
> On Wed, Dec 2, 2009 at 9:03 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>
>> Dear francesco:
>>
>> I think the procedure to build a rbcg model should be basically the same as
>> an atomistic one.
>> 1 : obtain the coordinates for your membrane, or protein. This can be done
>> by coarse graining all-atom model using cgtools plugin.
>> 2 : solvate the system using cgsolvate.tcl
>> 3 : add ions to the system.
>> About your "cgsolvate.tcl" problem, I think the reason u get the error:
>> conflicting versions provided for package "solvate": 1.3, then 1.2.
>> is not because the conflict with VMD 1.8.7, but you already type "package
>> require solvate" before the command "source ${script_dir}/cgsolvate.tcl".
>> Try to open a new fresh VMD console, and type "source
>> ${script_dir}/cgsolvate.tcl".
>>
>
> Dear Bin:
>
> Unless I misunderstood your suggestions, Anton's cgsolvate.tcl
> requires version 1.2 of "solvate", while VMD 1.8.7 has version 1.3. It
> seems to me that (as Anton suggested) the only chance to use that
> cgsolvate.tcl is installing an older version of VMD (see below).
>
> Please check what I did in order to rule out any mistake from my side:
>
> (1) Launch vmd 1.8.7
>
> (2) Load psf and pdb of my protein
>
> (3) Exten ... Tkcons ...source ${working_directory}cgsolvate.tcl
> conflicting versions provided for package "solvate": 1.3; then 1.2
>
>
> I had to place cgtools in the same dir as the psf pdb of my molecule.
> If it in another dir (specified as you indicated in the .tcl):
>
> can't read "/home/francesco/scripts_param/vmd/Anton" no such variable.
> Typing "package require solvate" before sourcing cgsolvate.tcl: same
> error.
>
> Looking at Anton's cgsolvate.tcl:
>
> if { $num != 0 } {
> puts "Found $num water atoms near the solute! Please report this bug to"
> puts "vmd_at_ks.uiuc.edu, including, if possible, your psf and pdb file."
> error "Solvate 1.2 failed."
> }
> puts "Solvate 1.2 completed successfully."
> return [list $min $max]
> }
>
>
> is it possible to simply replace "Solvate 1.2" with "Solvate 1.3"? I
> guess NO, otherwise Anton would have already suggested that.
>
>
> Please notice that I am using VMD version 1.8.7 for amd64; this means
> (as relevant or unrelevant as it might be) that (under Debian Linux
> amd64) there are two tcl directories
>
> /usr/local/lib/vmd/plugins/LINUXAMD64/tcl/autopsf1.2 etc.
>
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0
>
> /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.3
>
> I have recently upgraded to vmd 1.8.7, saving previous installed files
> of vmd 1.8.6 by renaming "local" "original_local):
>
> /usr/original_local/lib/vmd/plugins/noarch/tcl/solvate1.2
> /usr/original_local/lib/vmd/plugins/noarch/tcl/solvate1.2/pkgIndex.tcl
> /usr/original_local/lib/vmd/plugins/noarch/tcl/solvate1.2/solvate.tcl
> /usr/original_local/lib/vmd/plugins/noarch/tcl/solvate1.2/wat.pdb
> /usr/original_local/lib/vmd/plugins/noarch/tcl/solvate1.2/wat.psf
> /usr/original_local/lib/vmd/plugins/noarch/tcl/solvate1.2/wat.top
>
> /usr/original_local/lib/vmd/plugins/noarch/tcl/cgtools1.0
> /usr/original_local/lib/vmd/plugins/noarch/tcl/cgtools1.0/cggui.tcl
> /usr/original_local/lib/vmd/plugins/noarch/tcl/cgtools1.0/cgnetworking.tcl
> /usr/original_local/lib/vmd/plugins/noarch/tcl/cgtools1.0/cgtools.tcl
> /usr/original_local/lib/vmd/plugins/noarch/tcl/cgtools1.0/pkgIndex.tcl
> /usr/original_local/lib/vmd/plugins/noarch/tcl/cgtools1.0/protein.cgc
> /usr/original_local/lib/vmd/plugins/noarch/tcl/cgtools1.0/water.cgc
>
> Comparing the above content of cgtools1.0 (vmd 1.8.6) with that for vmd 1.8.7
>
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/cggui.tcl
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/cgnetworking.tcl
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/cgtools.tcl
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/pkgIndex.tcl
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/protein.cgc
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.par
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.top
> /usr/local/lib/vmd/plugins/noarch/tcl/cgtools1.0/water.cgc
>
>
> do you think there is any chance to carry out the whole job with VMD
> 1.8.6 (or can partly 1.8.6, partly 1.8.7 be used)? Clearly, the ideal
> would be to update Anton's scripts (cgsolvate.tcl and others if
> needed) to VMD 1.8.7. I would do that if I were a capable developer,
> which, unfortunately, I am not. Is anyone needing those scripts
> willing to do that? I can't imagine how much time it will take.
>
> thanks
>
> francesco
>
>
>
>
>> But you do need to change the following lines in the cgsolvate.tcl file to
>> provide correct directory:
>> 154 readpsf /Projects/anton/ReducedModels/CG/dat/CGSOLV/cgwat.psf
>> 155 coordpdb /Projects/anton/ReducedModels/CG/dat/CGSOLV/cgwat.pdb
>> 194 topology /home/amyshih/CGSOLV/water.top
>> Hope this helps,
>> Bin
>> On Dec 2, 2009, at 10:13 AM, Francesco Pietra wrote:
>>
>> Hi;
>> After I posted the subject problem as secondary matter, I carried out
>> an accurate search on the web, unable to find an equilibrated rbcg
>> lipid bilayer for vmd 1.8.7/namd martini implementation (or a plain
>> procedure to get it from scratch). As for sbcg, I guess that direct
>> conversion from an equilibrated all-atoms lipid bilayer will not work.
>> Thanks for info.
>> francesco pietra
>>
>>
>>