VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jul 17 2018 - 09:52:42 CDT

Please check out some real charmm toplogy files for how these things are
supposed to look; you are at the very least missing a RESI line as
suggested in my previous email, an END line, and likely MASS definitions
for many of the types used here.
Best,
Peter

On Tue, Jul 17, 2018 at 10:47 AM, Stamatia Zavitsanou <
zavitsanoustamatia_at_gmail.com> wrote:

> ATOM CAQ C1AQ -0.161
> ATOM CAP C1AP -0.055
> ATOM NAO N1AO -0.522
> ATOM CAN C1AN 0.237
> ATOM CAM C1AM -0.282
> ATOM CAL C1AL -0.196
> ATOM CAA C1AA -0.237
> ATOM CAB C1AB -0.255
> ATOM CAC C1AC 0.093
> ATOM CAD C1AD -0.031
> ATOM CAE C1AE -0.192
> ATOM CAF C1AF -0.016
> ATOM NAG N1AG -0.542
> ATOM CAH C1AH 0.447
> ATOM OAR O1AR -0.427
> ATOM CAI C1AI 0.018
> ATOM CAJ C1AJ -0.123
> ATOM CAK C1AK -0.086
> ATOM CAU C1AU -0.168
> ATOM CAT C1AT -0.082
> ATOM CAS C1AS 0.169
> ATOM FAV F1AV -0.217
> ATOM H11 H111 0.090
> ATOM H12 H112 0.090
> ATOM H13 H113 0.090
> ATOM H14 H114 0.372
> ATOM H15 H115 0.193
> ATOM H16 H116 0.196
> ATOM H17 H117 0.196
> ATOM H18 H118 0.199
> ATOM H19 H119 0.090
> ATOM H20 H120 0.090
> ATOM H21 H121 0.090
> ATOM H22 H122 0.090
> ATOM H23 H123 0.311
> ATOM H24 H124 0.115
> ATOM H25 H125 0.115
> ATOM H26 H126 0.115
> ATOM H00 H100 0.186
> ATOM N11 N111 -0.53
> ATOM C11 C111 -0.092
> ATOM CLL CL11 -0.166
> ATOM H29 H129 0.352
> BOND CAQ H11
> BOND CAQ H12
> BOND CAQ H13
> BOND CAQ CAP
> BOND CAP NAO
> BOND CAP CAD
> BOND NAO H14
> BOND NAO CAN
> BOND CAN CAM
> BOND CAN CAC
> BOND CAM H15
> BOND CAM CAL
> BOND CAL H16
> BOND CAL CAA
> BOND CAA H17
> BOND CAA CAB
> BOND CAB H18
> BOND CAB CAC
> BOND CAC CAD
> BOND CAD CAE
> BOND CAE H19
> BOND CAE H20
> BOND CAE CAF
> BOND CAF H21
> BOND CAF H22
> BOND CAF NAG
> BOND NAG H23
> BOND NAG CAH
> BOND CAH OAR
> BOND CAH CAI
> BOND CAI CAJ
> BOND CAI CAS
> BOND CAJ H24
> BOND CAJ CAK
> BOND CAK H25
> BOND CAK CAU
> BOND CAU H26
> BOND CAU CAT
> BOND CAT H00
> BOND CAT CAS
> BOND CAS FAV
> BOND N11 H29
> BOND N11 CAN
> BOND C11 CLL
> BOND C11 CAL
> BOND CAN C11
> BOND CAP N11
>
>
>
> Matina
>
> On 17 July 2018 at 17:37, Peter Freddolino <petefred_at_umich.edu> wrote:
>
>> Could you post your hybrid.rtf file? It is clearly not liking something
>> there. Based on the error output I am guessing that you are missing the
>> RESI line.
>> Best,
>> Peter
>>
>> On Tue, Jul 17, 2018 at 9:56 AM, Stamatia Zavitsanou <
>> zavitsanoustamatia_at_gmail.com> wrote:
>>
>>> Dear Peter,
>>>
>>> Thank you for answering,
>>>
>>> Here is the error that autopsf gives when I try to "Create the chains"
>>> having loaded "toppar_water_ions_namd.str", "top_all36_cgenff.rtf" and the
>>> hybrid.rtf file I have created.
>>>
>>> ERROR: failed on end of segment
>>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>>> ERROR: failed on end of segment
>>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>>> while executing
>>> "segment $segid {
>>> pdb $segfile
>>>
>>> # We alias the C-terminal OXT atoms to OT2 so that psfgen has to
>>> guess one atom less.
>>> # Otherwise psf..."
>>> (procedure "psfsegments" line 37)
>>> invoked from within
>>> "psfsegments $logfileout"
>>> (procedure "::autopsf::afterchains_gui" line 66)
>>> invoked from within
>>> "::autopsf::afterchains_gui"
>>> invoked from within
>>> ".autopsf.chains.finish invoke"
>>> ("uplevel" body line 1)
>>> invoked from within
>>> "uplevel #0 [list $w invoke]"
>>> (procedure "tk::ButtonUp" line 22)
>>> invoked from within
>>> "tk::ButtonUp .autopsf.chains.finish"
>>> (command bound to event)
>>>
>>> When I do it with -dispdev text -e psfgen (where psfgen is the text
>>> below)
>>>
>>> mol delete all
>>> mol load pdb /home/matina/Desktop/CGenff/complex007.pdb
>>> set chainA [atomselect top "chain A and not hydrogen"]
>>> set chainB [atomselect top "chain B and not hydrogen"]
>>> set chainX [atomselect top "residuetype nothing"]
>>> $chainA writepdb chainA.pdb
>>> $chainB writepdb chainB.pdb
>>> $chainX writepdb chainX.pdb
>>> package require psfgen
>>> topology /home/matina/Desktop/CGenff/top_all36_cgenff.rtf
>>> topology /home/matina/Desktop/CGenff/toppar_water_ions_namd.str
>>> topology /home/matina/Desktop/CGenff/hybrid007.rtf
>>> pdbalias HIS HSD
>>> pdbalias atom SER HG HG1
>>> pdbalias residue HIS HSE
>>> pdbalias atom ILE CD1 CD
>>> segment A {
>>> first NONE
>>> last NONE
>>> pdb chainA.pdb
>>> }
>>>
>>> segment B {
>>> first NONE
>>> last NONE
>>> pdb chainB.pdb
>>> }
>>>
>>> segment X {
>>> first NONE
>>> last NONE
>>> pdb chainX.pdb
>>> }
>>>
>>> coordpdb chainA.pdb A
>>> coordpdb chainB.pdb B
>>> coordpdb chainX.pdb X
>>>
>>> guesscoord
>>> writepdb psf-complex.pdb
>>> writepsf psf-complex.psf
>>> exit
>>>
>>> I get this
>>>
>>> reading topology file /home/matina/Desktop/CGenff/hybrid007.rtf
>>>
>>> psfgen) ERROR! FAILED TO RECOGNIZE ATOM. Line 1: ATOM CAQ C1AQ
>>> -0.161
>>>
>>> psfgen) no residue in progress for atom
>>> psfgen) ERROR! Failed to parse atom statement. Line 2: ATOM CAP C1AP
>>> -0.055
>>>
>>> psfgen) no residue in progress for atom
>>> psfgen) ERROR! Failed to parse atom statement. Line 3: ATOM NAO N1AO
>>> -0.522
>>>
>>> psfgen) no residue in progress for atom
>>> psfgen) ERROR! Failed to parse atom statement. Line 4: ATOM CAN C1AN
>>> 0.237
>>> .........
>>>
>>> psfgen) no residue in progress for bond
>>> psfgen) ERROR! Failed to parse bond statement. Line 44: BOND CAQ H11
>>>
>>> psfgen) no residue in progress for bond
>>> psfgen) ERROR! Failed to parse bond statement. Line 45: BOND CAQ H12
>>>
>>> psfgen) no residue in progress for bond
>>> psfgen) ERROR! Failed to parse bond statement. Line 46: BOND CAQ H13
>>>
>>> psfgen) no residue in progress for bond
>>> psfgen) ERROR! Failed to parse bond statement. Line 47: BOND CAQ CAP
>>> ................
>>>
>>> psfgen) aliasing residue SER atom HG to HG1
>>> psfgen) aliasing residue HIS to HSE
>>> psfgen) aliasing residue ILE atom CD1 to CD
>>> psfgen) building segment A
>>> psfgen) setting patch for first residue to NONE
>>> psfgen) setting patch for last residue to NONE
>>> psfgen) reading residues from pdb file chainA.pdb
>>> psfgen) unknown residue type MET
>>> psfgen) unknown residue type ALA
>>> psfgen) unknown residue type GLY
>>> psfgen) unknown residue type ARG
>>> psfgen) unknown residue type LEU
>>> psfgen) unknown residue type PRO
>>> .....................
>>> psfgen) extracted 418 residues from pdb file
>>> psfgen) Info: generating structure...psfgen) unknown residue type MET
>>> failed!
>>> ERROR: failed on end of segment
>>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>>
>>> MOLECULE MISSING! Use resetpsf to start over.
>>> Info) VMD for LINUXAMD64, version 1.9.4a12 (December 21, 2017)
>>> Info) Exiting normally.
>>>
>>> Thank you again,
>>> Matina
>>>
>>>
>>> On 17 July 2018 at 16:00, Peter Freddolino <petefred_at_umich.edu> wrote:
>>>
>>>> Dear Matina,
>>>> It would be helpful to paste the error output that you get from VMD
>>>> when you try to run this. Chances are it is having trouble with your
>>>> topology file, but without more information it is impossible to guess what
>>>> is going on.
>>>> Thanks,
>>>> Peter
>>>>
>>>>
>>>> On Tue, Jul 17, 2018 at 4:59 AM, Stamatia Zavitsanou <
>>>> zavitsanoustamatia_at_gmail.com> wrote:
>>>>
>>>>> Hello,
>>>>> I am trying to generate a PSF file in order to run a NAMD/FEP
>>>>> simulation.
>>>>> I use input from CGenFF.
>>>>> I have created the dual topology file (hybrid.rtf which is created
>>>>> after I have merged the reference with the mutant ligand into one file) and
>>>>> the complex.pdb file of the protein and the two ligands.
>>>>> I want to use autopsf and I load the complex.pdb file, the topology of
>>>>> the two ligands, hybrid.rtf file and these two files that I have found from
>>>>> CGenFF, toppar_water_ions_namd.str, top_all36_cgenff.rtf. Is this correct?
>>>>> It only creates a complex007_autopsf-temp.pdb not a final I think it's
>>>>> because VMD cannot read my hybrid.rtf file. Has anyone tried to do anything
>>>>> like that?
>>>>>
>>>>> If not how do you create the PSF file to run a NAMD/FEP simulation?
>>>>>
>>>>> Thank you,
>>>>> Matina
>>>>>
>>>>
>>>>
>>>
>>
>