VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Fri Sep 01 2017 - 08:19:06 CDT

Dear Amin,

the error seems to be due to the space in the folder's name "2-THR
THR2ALA". Did you, by any chance, included a space in the any folder's
name? Does this happen if you select a different residue?

thank you for reporting these issues

Best

João

On Fri, Sep 1, 2017 at 4:46 AM amin sagar <aamin.sagar_at_gmail.com> wrote:

> Thanks a lot for the suggestion. I moved one step ahead. Now, the error I
> get is -
>
> Unable to load structure file
> /home/srlab/amin/Simulations/SLT1/FEP-try/SLT1_QwikMD-FEP/2-THR
> THR2ALA/Host-Guest/2.fep.psf
>
> while executing
> "mol load psf
> $dirpath/$eachres-$resnamedir$tempala/Host-Guest/$eachres.fep.psf pdb
> $dirpath/$eachres-$resnamedir$tempala/Host-Guest/$eachres.fep"
> (procedure "::alascan::mutator" line 270)
> invoked from within
> "::alascan::mutator"
> invoked from within
> ".alascangui.fep.write invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .alascangui.fep.write"
> (command bound to event)
>
> The psf and pdb files are written in the directory it is searching for the
> psf file but no NAMD config files are written.
>
> Also I get the warning
>
> Alanine scan: WARNING - unexpected atom name OG1: belongs to a patch?
> Alanine scan: WARNING - unexpected atom name HG1: belongs to a patch?
> Alanine scan: WARNING - unexpected atom name CG2: belongs to a patch?
> Alanine scan: WARNING - unexpected atom name HG21: belongs to a patch?
> Alanine scan: WARNING - unexpected atom name HG22: belongs to a patch?
> Alanine scan: WARNING - unexpected atom name HG23: belongs to a patch?
>
> These atoms belong to whatever residue I choose to mutate to Ala.
>
> Can I please get some more help. I would be really thankful.
>
> Regards,
> Amin.
>
>
>
> On Thu, Aug 31, 2017 at 8:27 PM, João Ribeiro <jribeiro_at_ks.uiuc.edu>
> wrote:
>
>> Dear Amin,
>>
>> QwikMD uses autopsf to generate psf and pdbs. As you saw and JC
>> mentioned, replacing the temporary topology file used by autopsf listed on
>> the REMARKS (*_formatted_autopsf-temp.top) by your local topology files
>> gives psfgen the information regarding your protein.
>>
>> One thing that you can do is to copy the contents of top_all36_hybrid.inp
>> (located in the folder of the readcharmmtop plugin - $env(CHARMMTOPDIR)) to
>> the top_all36_prot.rtf file. Paste the content after all the topologies
>> listed in top_all36_prot.rtf file, but before the keyword "END". To make
>> sure that this hack does not influence other simulations that you may
>> prepare in the future, save this new topology file using a different name
>> and save in a local folder. Add this new file to the remarks of the psf
>> file and in principle the errors will be fixed. Please review your
>> structure carefully after building the structure and have a critical view
>> of the results.
>>
>> The errors regarding the missing residues occur during the building of
>> the non-protein pdb file, and those residues are protein residues. I would
>> assume that there is not problem in that regard, but, once again, please
>> check your structure and see if the terminals of the protein are being
>> created properly.
>>
>> I hope this helps
>>
>> Best
>>
>> João
>>
>> On Thu, Aug 31, 2017 at 1:29 AM amin sagar <aamin.sagar_at_gmail.com> wrote:
>>
>>> Thanks for the suggestion. I added those REMARKS to the psf file and now
>>> I don't get those "Unknown residue type" errors. However I still get the
>>> error that the first and last residue don't exist. I have checked that they
>>> do exist in both PDB and PSF. I have posted the error below.
>>>
>>> I made the psf file using QuikMD, is it possible that this file is not
>>> compatible with Alanine scanning plugin?
>>>
>>> I also get the error that Residue V2A is not unknown but that residue is
>>> present in the hybrid topology file.
>>>
>>> I would really be thankful for more suggestions.
>>>
>>>
>>> Structure requires EXTended PSF format
>>> psfgen) total of 0 cross-terms
>>> psfgen) no residue 145 of segment AP1
>>> psfgen) Residue AP1:145 not exsisting, skipping patch CTER.
>>>
>>> psfgen) no residue 1 of segment AP1
>>> psfgen) Residue AP1:1 not exsisting, skipping patch NTER.
>>>
>>> psfgen) no residue 145 of segment BP1
>>> psfgen) Residue BP1:145 not exsisting, skipping patch CTER.
>>>
>>> psfgen) no residue 1 of segment BP1
>>> psfgen) Residue BP1:1 not exsisting, skipping patch NTER.
>>>
>>> psfgen) Info: psf file complete.
>>> psfgen) Info: writing pdb file
>>> /home/srlab/amin/Simulations/SLT1/FEP-try/SLT1_QwikMD-FEP/4-VAL
>>> VAL2ALA/mtemp-nprot.pdb
>>> psfgen) Info: pdb file complete.
>>> psfgen) clearing structure, preserving topology and aliases
>>> psfgen) building segment AP1
>>> psfgen) reading residues from pdb file
>>> /home/srlab/amin/Simulations/SLT1/FEP-try/SLT1_QwikMD-FEP/4-VAL
>>> VAL2ALA/mtemp-AP1.pdb
>>> psfgen) extracted 145 residues from pdb file
>>> psfgen) setting patch for first residue to NONE
>>> Alanine scan: Residue VAL 4 of segment AP1 is mutated to V2A
>>> psfgen) mutating residue 4 from VAL to V2A
>>> psfgen) unknown residue type V2A
>>> psfgen) setting patch for last residue to NONE
>>> psfgen) Info: generating structure...psfgen) unknown residue type V2A
>>>
>>> Regards,
>>> Amin
>>>
>>> On Wed, Aug 30, 2017 at 6:10 AM, JC Gumbart <gumbart_at_physics.gatech.edu>
>>> wrote:
>>>
>>>> This plugin reads the top of your PSF to determine other topology files
>>>> it should load. If your psf wasn’t generated by psfgen it may be missing
>>>> these lines. So add a line like
>>>> REMARKS topology
>>>> /Users/gumbart/Documents/Research/toppar/top_all36_prot.rtf
>>>> that points to the necessary topology file(s).
>>>>
>>>> However, this created a different error that required me modifying the
>>>> plugin code, but then I got no output. So at this point I gave up.
>>>> Hopefully someone else can chime in.
>>>>
>>>> Best,
>>>> JC
>>>>
>>>
>>>> > On Aug 29, 2017, at 9:37 AM, amin sagar <aamin.sagar_at_gmail.com>
>>>> wrote:
>>>> >
>>>> > Dear All,
>>>> > I am trying to setup an Alanine scanning FEP simulation using the
>>>> Alanine Scanning Plugin. I am getting " psfgen) unknown residue type " for
>>>> all the residues.
>>>> >
>>>> > I loaded the psf, pdb and xsc files from an earlier simulation in
>>>> which the system has my protein, ligand, water and the ions. Are these the
>>>> correct kind of files?
>>>> >
>>>>
>>> > I am adding all the par_all36* parameters and selecting the
>>>> top_all36.... hybrid topology file.
>>>>
>>>
>>>> >
>>>> > I have pasted the first and the last part of the error message below--001a114aa474a215d30558209bfe--