VMD-L Mailing List

From: Stamatia Zavitsanou (zavitsanoustamatia_at_gmail.com)
Date: Tue Jul 17 2018 - 09:47:20 CDT

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
>>>>
>>>
>>>
>>
>