Hello Thomas,
actually yes, it may be the source of the problem.
Could you precise what is the advantage to loading the rst file ?
Normally I use pdb and the topology in the same time, e.g.
vmd -parm7 output.prmtop output.pdb
Thank you in advance !
Enrico
Il giorno mer 19 lug 2023 alle ore 08:45 Steinbrecher, Thomas
<thomas.steinbrecher.roche.com> ha scritto:
>
> Hi Enrico,
>
> is it possible that loading your file in vmd has a off-by-one error from the format? Amber rst, rst7, crd and crdbox files sometimes can be loaded with the wrong format specified but then bonds are shifted by one. Does vmd -parm7 XXX -rst7 YYY look like?
>
> Kind Regards,
>
> Thomas
>
> On Tue, Jul 18, 2023 at 2:41 PM Enrico Martinez via AMBER <amber.ambermd.org> wrote:
>>
>> P.S. you may use it directly from the terminal in the following way
>> vmd -parm7 output.prmtop output.pdb
>>
>> :-)
>>
>> Il giorno mar 18 lug 2023 alle ore 14:36 Enrico Martinez
>> <jmsstarlight.gmail.com> ha scritto:
>> >
>> > Right, I gotcha thank you very much Carlos!
>> >
>> > With best regards
>> >
>> > Enrico
>> >
>> > Il giorno mar 18 lug 2023 alle ore 12:53 Carlos Simmerling
>> > <carlos.simmerling.gmail.com> ha scritto:
>> > >
>> > > Yes it's always safest to load the prmtop first, then Vmd will use the actual bond list. I do it through the gui, not sure about command line options.
>> > >
>> > > On Tue, Jul 18, 2023, 6:52 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>> > >>
>> > >> Yep exactly, I still see the longer bond when I load it in pymol, so
>> > >> probably it is a problem of visualisation ..
>> > >>
>> > >> But actually this is a good idea to load prmtop additionally in vmd.
>> > >> Is it possible to do it directly in the linux terminal something like
>> > >> vmd -parmtop input.parmtop input.pdb ?
>> > >>
>> > >> Il giorno mar 18 lug 2023 alle ore 12:37 Carlos Simmerling
>> > >> <carlos.simmerling.gmail.com> ha scritto:
>> > >> >
>> > >> > I re-ran the tleap script using the new pdb (which also removes the small molecules that were missing parameters).
>> > >> > it seems to work fine with no errors, and I do not get any long bonds in vmd when I visualize either the output pdb or the prmtop/crd combination.
>> > >> > perhaps the long bond is a visualization artifact in your program?
>> > >> > I am attaching the output pdb for you to compare to yours.
>> > >> >
>> > >> > On Tue, Jul 18, 2023 at 6:24 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>> > >> >>
>> > >> >> ops again sorry, actually this is a correct pbd BUT I forgot to remove
>> > >> >> hydrogens from the pdb, no comments .. !
>> > >> >>
>> > >> >> Here it is, I've just checked it via tleap - it prepares all the
>> > >> >> filles for amber but in the created PBD I see this unnatural bond ..
>> > >> >>
>> > >> >> Il giorno mar 18 lug 2023 alle ore 12:08 Carlos Simmerling
>> > >> >> <carlos.simmerling.gmail.com> ha scritto:
>> > >> >> >
>> > >> >> > I spent some time working on this, but it turns out that this cannot be the input that you used.
>> > >> >> > the pdb file name doesn't match the one in the tleap script, and even if I rename it, tleap fails with errors because it doesn't have the force field library files for molecules in that pdb file.
>> > >> >> >
>> > >> >> > the pdb file that you sent appears reasonable to me, with a TER between the 2 peptide chains.
>> > >> >> >
>> > >> >> > as a side note, this structure appears unusual to me, I would not expect it to be stable in solution in this conformation. I would look closely at the crystal packing and interpret the MD with caution. Of course you know much more about this system, I just wanted to point out my concern in case you hadn't considered it.
>> > >> >> > carlos
>> > >> >> >
>> > >> >> > On Tue, Jul 18, 2023 at 4:15 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>> > >> >> >>
>> > >> >> >> Dear friends,
>> > >> >> >>
>> > >> >> >> ops sorry I did not see the update of the topic.
>> > >> >> >> Please find enclosed my tleap script and attached the input pdb.
>> > >> >> >>
>> > >> >> >> source leaprc.protein.ff19SB
>> > >> >> >> source leaprc.water.opc
>> > >> >> >> prot = loadpdb input.pdb
>> > >> >> >> addIons prot Cl- 0
>> > >> >> >> addIons prot Na+ 0
>> > >> >> >> setbox prot centers
>> > >> >> >> solvateoct prot TIP3PBOX 20.0
>> > >> >> >> savepdb prot output_300K.pdb
>> > >> >> >> saveamberparm prot output.prmtop output.prmcrd
>> > >> >> >> quit
>> > >> >> >>
>> > >> >> >> So the unnatural bound was observed in the output_300K.pdb produced by
>> > >> >> >> the same tleap script.
>> > >> >> >>
>> > >> >> >> Yours with thanks
>> > >> >> >>
>> > >> >> >> Enrico
>> > >> >> >>
>> > >> >> >> Il giorno lun 10 lug 2023 alle ore 17:23 David A Case
>> > >> >> >> <david.case.rutgers.edu> ha scritto:
>> > >> >> >> >
>> > >> >> >> > On Fri, Jul 07, 2023, Enrico Martinez via AMBER wrote:
>> > >> >> >> >
>> > >> >> >> > >P.S. there is no tleap wartning in the output log regarding any long bounds.
>> > >> >> >> > >and the both chains are recognized correctly
>> > >> >> >> > > res total affected
>> > >> >> >> > >
>> > >> >> >> > > CARG 1
>> > >> >> >> > > CGLY 1
>> > >> >> >> > > NASP 1
>> > >> >> >> > > NGLY 1
>> > >> >> >> > > WAT 37077
>> > >> >> >> > >
>> > >> >> >> > >
>> > >> >> >> > >however when I open the complex in vmd or pymol I see a new bound
>> > >> >> >> > >between the N-terminal end of the peptide (chain B) and the N terminal
>> > >> >> >> > >end of the protein (chain A)
>> > >> >> >> >
>> > >> >> >> > You don't say how you "open[ed] the complex in vmd or pymol". Did you
>> > >> >> >> > generate a PDB-style file first? (If so, how?) It sounds like the extra
>> > >> >> >> > bond is a visualization artifact, but your use case is very odd: exactly
>> > >> >> >> > which atoms are involved in the N-termain (NASP?) to N-terminal (NGLY?)
>> > >> >> >> > bond?
>> > >> >> >> >
>> > >> >> >> > ...dac
>> > >> >> >> >
>>
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>
>
>
> --
> Dr. Thomas Steinbrecher
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
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Received on Wed Jul 19 2023 - 02:00:02 PDT
