From: Stamatia Zavitsanou (zavitsanoustamatia_at_gmail.com)
Date: Tue Jul 17 2018 - 10:16:30 CDT

Yes! Thank you!
About the MASS definitions, I thought that "top_all36_cgenff.rtf" was
supposed to assign them somehow.
I have only used LigParGen where everything was already there. I will try
to find a real charmm topology file as you suggested.

Thank you again,
Matina

On 17 July 2018 at 17:52, Peter Freddolino <petefred_at_umich.edu> wrote:

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