VMD-L Mailing List

From: amin sagar (aamin.sagar_at_gmail.com)
Date: Fri Sep 01 2017 - 08:33:17 CDT

Dear João,
Thanks for the response.
I also thought it might be because of space in the name. So, I tried to
load the psf file from the Tk console and also using the GUI. But it
doesn't load. Then I noticed that in the terminal, I was getting the error:
 Using plugin psf for structure file
/home/srlab/amin/Simulations/SLT1/FEP-manual/thr134ala.fep-ori.psf

psfplugin) Failed to parse segname in PSF file:
psfplugin) ' 1 AP1 1 MET N NH3
-0.300000 14.0070 0
'
couldn't read atom 0
ERROR) molecule_structure: Unable to read structure for molecule 0
ERROR) molecule_structure: severe error indicated by plugin aborting
loading of molecule 0

I tried adding EXT and CMAP to the first line of the psf file
Then the psf file gets loaded but still I get the following message.
Using plugin psf for structure file
/home/srlab/amin/Simulations/SLT1/FEP-manual/thr134ala.fep.psf
Bonds line too short in psf file:
       1 5 2 1 3 1 4 1

psfplugin) ERROR: unable to read the specified number of bonds!
psfplugin) Expected 28686 bonds but only read 0
ERROR) Error reading bond information.
psfplugin) WARNING: no angles defined in PSF file.
psfplugin) WARNING: no dihedrals defined in PSF file.
psfplugin) WARNING: no impropers defined in PSF file.
psfplugin) no cross-terms defined in PSF file.
Info) Analyzing structure ...
Info) Atoms: 40872
Info) Bonds: 0
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 40872
Info) Waters: 36474
Info) Segments: 14
Info) Fragments: 40872 Protein: 0 Nucleic: 0

I think these warnings are serious. Can you please suggest something about
this as well.

Regards,
Amin.

On Fri, Sep 1, 2017 at 6:49 PM, João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> 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.
>>>>> >
>>>>> > I would be really thankful for any help.
>>>>> >
>>>>> > Regards.
>>>>> > Amin.
>>>>> >
>>>>> >
>>>>> > psfgen) total of 45211 atoms
>>>>> > psfgen) total of 30094 bonds
>>>>> > psfgen) total of 15107 angles
>>>>> > psfgen) total of 132 dihedrals
>>>>> > psfgen) total of 0 impropers
>>>>> > psfgen) total of 0 explicit exclusions
>>>>> > psfgen) 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/2-THR THR2ALA/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/2-THR THR2ALA/mtemp-AP1.pdb
>>>>> > psfgen) unknown residue type MET
>>>>> > psfgen) unknown residue type THR
>>>>> > psfgen) unknown residue type LEU
>>>>> > psfgen) unknown residue type VAL
>>>>> > psfgen) unknown residue type LYS
>>>>> > psfgen) unknown residue type ILE
>>>>> > ..
>>>>> > ..
>>>>> > psfgen) unknown residue type HSD
>>>>> > psfgen) unknown residue type PRO
>>>>> > psfgen) extracted 145 residues from pdb file
>>>>> > psfgen) setting patch for first residue to NONE
>>>>> > Alanine scan: Residue THR 2 of segment AP1 is mutated to T2A
>>>>> > psfgen) mutating residue 2 from THR to T2A
>>>>> > psfgen) unknown residue type T2A
>>>>> > psfgen) setting patch for last residue to NONE
>>>>> > psfgen) Info: generating structure...psfgen) unknown residue type MET
>>>>> > failed!
>>>>> >
>>>>> >
>>>>>
>>>>> --
>>> ……………………………………………………...
>>> João Vieira Ribeiro
>>> Theoretical and Computational Biophysics Group
>>> Beckman Institute, University of Illinois
>>> jribeiro_at_ks.uiuc.edu
>>> +1 (217) 3000380 <(217)%20300-0380>
>>>
>>
>> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3000380
>