VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Nov 15 2007 - 09:44:00 CST

Hi Francesco,
just a couple notes:
-the appropriate name for epsilon protonated histidine in the charmm
forcefield is HSE, not HIE -- it probably is not recognizing this residue
-Likewise, your water should either be aliased or have a residue name
that is in your topology file, like TIP3
-As Axel noted, the presence of TER cards should not matter to psfgen;
it will treat each of your chains (each defined in a separate input pdb
file) separately and not generate bonds between them

Best,
Peter

Francesco Pietra wrote:
> axel:
> Yes, my posting was badly organized.
>
> combine.tcl is from http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
> I do not attach it here because my subsequent managing has shown that the
> problem is with protein.psf file. This is the result of not sticking to a
> single house. I use Amber9 for MD, DOCK6.1 for docking, Chimera for dockprep,
> and VMD for what that world is unable to do, or simply to have a better
> insight. That mixture would require a better general command than I have
> presently attained.
>
> I am working with a pore protein model that it took long to be fully in order
> for both Amber9 and DOCK6.1. The pdb file is absolutely standard (as far as VMD
> pluging are concerned, HIS is HIE and ILE has CD1). Present work in Generalized
> Born conditions is fully OK. A check with known ligands (treated with
> Antechamber) is OK, both with computations and experimental work.
>
> I tried both manual generation of the psf file according to tutorials at
> http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ and automatic generation
> from VMD Extensions..Modeling...Automatic PSF Builder. Both arrived at wrong
> psf. I am attaching the log from the last trial with Automatic generation (I
> have renamed the generated "protein_autopsf_tmpfile.psf" "protein.psf" when the
> former name failed). In both cases, "cross terms" are lacking from psf file.
> Must say that Autopsf has parameterized 8 instances of HIE (15 atoms each) and
> the single WAT (3 atoms) residue. The latter is for a (natural) molecule of
> water within the pore.
>
> Looking at protein_autopsf_tmpfile.pdb with Chimera, it is clear that the
> procedure has removed the three "TER" records that I had set to get rid of
> three 50A-long bonds (those long bonds are not revealed by VMD - at least not
> in my default use of it - though they hinder dockprep workind and, in any case,
> create problems to MD).
>
> Thanks
> francesco
>
>
>
> --- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
>
>> francesco,
>>
>> which version of combine.tcl (there must be hundreds of scripts
>> under that name. i have at least five on my machine) are you
>> using and how, if at all, did you modify it.
>>
>> by not showing the script code you were using, only those people
>> can help you, who know it and know which particular version you
>> are using. if you want to increase your chances to get help, you
>> have to help us by providing more information, even if they seem
>> redundant or obvious to you. it is very hard to give advice without
>> context.
>>
>> regards,
>> axel.
>>
>>
>> On 11/14/07, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
>>
>>> I am in a silly loop, trying to merge protein and POPC membrane and
>>>
>> removing
>>
>>> superimposition.
>>>
>>> I created a 100x100A POPC (less is not enough for my protein) and inserted
>>>
>> and
>>
>>> centered the protein.
>>>
>>> Saved protein_aligned.pdb. fed to the working directory both scripts
>>> combine.tcl and top_all27_prot_lipid.inp.
>>>
>>> The, at
>>>
>>> vmd -dispdev text < combine.tcl |tee combine.log
>>>
>>
>>
>>> the error was:
>>>
>>> There is no 'top' molecule in atom select's 'molId' (VMD 1.8.6).
>>>
>>> After resetpsf, I tried various (clearly faulty) selections with no
>>>
>> success.
>>
>>> Thanks for helping
>>> francesco pietra
>>>
>>> Incidentally, does 10x100 cause steric clashes?
>>>
>>>
>>>
>>>
> ____________________________________________________________________________________
>
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>>>
>> --
>> =======================================================================
>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
>> Center for Molecular Modeling -- University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>> =======================================================================
>> If you make something idiot-proof, the universe creates a better idiot.
>>
>>
>
>
>
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