From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Jun 27 2014 - 10:37:19 CDT
With all due respect, I'm getting a headache looking at this. Maybe I'm
missing something, but it looks like it would have been *so* much simpler
to define the staple as a patch that links to lysines together, *exactly*
like the existing disufide patch that links two cysteines together. No
gigantic residue, no complicated patching together of the backbone, no
CMAP worries... just one single simple patch.
To illustrate how error-prone your approach is, patching together the
backbone using your patches will remove the CMAP on adjacent residues (or
at least in CHARMM, it would). Also, I'm not sure the "3" in PRES CMPS is
supported at all. That's just two issues I can see from the top of my
head; there likely are more, as illustrated by the error this discussion
thread started with. I really think this is not a good approach.
I'm extremely busy right now but I can probably help you next week (on
this list) with putting together a disulfide-like patch. It won't be much
work; it's really exceedingly simple.
By the way, we strongly discourage editing existing topology and parameter
files. Edited version have a way to eventually fall into the hands of an
unsuspecting user and wreck havoc. It would be cleaner to create a
separate topology and (if necessary) parameter file for your staple.
On 06/27/2014 10:29 AM, Douglas Houston wrote:
> Hi Tristan,
>
> Yes, you've got it. The CMPS patch is the CHARMM36 CMAP potential for the
> end of the staple - every amino acid residue in the CHARMM36 topology file
> (top_all36_prot.rtf) seems to have one so I assumed it was appropriate.
>
> The reason I did it this way was because I had example patches I could
> modify - I wouldn't know how to write a patch that linked the the two
> copies together at their terminal carbons as you suggest (note the double
> bond in the middle).
>
> One thing that I was unsure about was the IC tables - each amino acid
> residue has one of these but I didn't create one for my OL1 residue. I
> thought using "regenerate angles dihedrals" in psfgen accomplished the
> same thing?
>
> Here are the relevant entries in my modified .rtf topology file:
>
> RESI OL1 0.00
> GROUP
> ATOM N NH1 -0.47 ! |
> |
> ATOM HN H 0.31 ! HN-N
> NL-HNL
> ATOM CA CT1 0.16 ! HB1 | HH1 HG1 HD1 HE1 HP1 HZL1 HDL1
> HGL1 HHL1 | HBL1
> ! \ | | | | | | | |
> | | | /
> GROUP
> !HB2-CB-CA--CH--CG--CD--CE--CP--CZL==CEL--CDL--CGL--CHL--CAL--CBL-HBL2
> ATOM CB CT3 -0.27 ! / | | | | | | | |
> | | | \
> ATOM HB1 HA3 0.09 ! HB3 | HH2 HG2 HD2 HE2 HP2 HEL1 HDL2
> HGL2 HHL2 | HBL3
> ATOM HB2 HA3 0.09 ! O=C
> CL=OL
> ATOM HB3 HA3 0.09 ! |
> |
> GROUP !
> ATOM C C 0.51
> ATOM O O -0.51
> GROUP
> ATOM CH CT2 -0.18 !
> ATOM HH1 HA2 0.09 !
> ATOM HH2 HA2 0.09 !
> GROUP
> ATOM CG CT2 -0.18 !
> ATOM HG1 HA2 0.09 !
> ATOM HG2 HA2 0.09 !
> GROUP
> ATOM CD CT2 -0.18 !
> ATOM HD1 HA2 0.09 !
> ATOM HD2 HA2 0.09 !
> GROUP
> ATOM CE CT2 -0.18 !
> ATOM HE1 HA2 0.09 !
> ATOM HE2 HA2 0.09 !
> GROUP
> ATOM CP CT2 -0.18 !
> ATOM HP1 HA2 0.09 !
> ATOM HP2 HA2 0.09 !
> GROUP
> ATOM CZL CEL1 -0.15 !
> ATOM HZL1 HEL1 0.15 !
> GROUP
> ATOM CEL CEL1 -0.15 !
> ATOM HEL1 HEL1 0.15 !
> GROUP
> ATOM CDL CT2 -0.18 !
> ATOM HDL1 HA2 0.09 !
> ATOM HDL2 HA2 0.09 !
> GROUP
> ATOM CGL CT2 -0.18 !
> ATOM HGL1 HA2 0.09 !
> ATOM HGL2 HA2 0.09 !
> GROUP
> ATOM CHL CT2 -0.18 !
> ATOM HHL1 HA2 0.09 !
> ATOM HHL2 HA2 0.09 !
> GROUP
> ATOM NL NH1 -0.47 ! |
> |
> ATOM HNL H 0.31 ! HN-N
> NL-HNL
> ATOM CAL CT1 0.16 ! HB1 | HH1 HG1 HD1 HE1 HP1 HZL1 HDL1
> HGL1 HHL1 | HBL1
> ! \ | | | | | | | |
> | | | /
> GROUP
> !HB2-CB-CA--CH--CG--CD--CE--CP--CZL==CEL--CDL--CGL--CHL--CAL--CBL-HBL2
> ATOM CBL CT3 -0.27 ! / | | | | | | | |
> | | | \
> ATOM HBL1 HA3 0.09 ! HB3 | HH2 HG2 HD2 HE2 HP2 HEL1 HDL2
> HGL2 HHL2 | HBL3
> ATOM HBL2 HA3 0.09 ! O=C
> CL=OL
> ATOM HBL3 HA3 0.09 ! |
> |
> GROUP !
> ATOM CL C 0.51
> ATOM OL O -0.51
> BOND CH CA CG CH CD CG CE CD CP CE
> BOND CZL CP CDL CEL CGL CDL CHL CGL
> BOND CAL CHL CZL HZL1 CEL HEL1 CDL HDL1 CDL HDL2
> BOND CGL HGL1 CGL HGL2 CHL HHL1 CHL HHL2
> BOND CH HH1 CH HH2 CG HG1 CG HG2 CD HD1
> BOND CD HD2 CE HE1 CE HE2
> BOND CP HP1 CP HP2
> BOND CB CA N HN N CA
> BOND CBL CAL NL HNL NL CAL
> BOND C CA C +N CB HB1 CB HB2 CB HB3
> BOND CL CAL CBL HBL1 CBL HBL2 CBL HBL3
> DOUBLE O C OL CL
> DOUBLE CZL CEL
> IMPR N -C CA HN C CA +N O
> CMAP -C N CA C N CA C +N
> DONOR HN N
> DONOR HNL NL
> ACCEPTOR O C
> ACCEPTOR OL CL
>
>
> PRES CMPS 0.00 ! CMAP potential for end of staple
> ! 1 refers to previous (N terminal)
> ! 2 refers to staple
> ! 3 refers to next (C terminal)
> ! use in a patch statement
> CMAP 1C 2NL 2CAL 2CL 2NL 2CAL 2CL 3N
>
>
> PRES STCN 0.00 ! linkage for joining staple (atom names end in L)
> with backbone - pre-staple
> ! 1 refers to previous (N terminal)
> ! 2 refers to next (C terminal)
> ! use in a patch statement
> DELETE IMPR 2N 1C 2CA 2HN !Improper specified by IMPR N -C CA HN
> DELETE IC 1C 2CA *2N 2HN!Specified by IC -C CA *N HN
> BOND 1C 2NL
> IMPR 2NL 1C 2CAL 2HNL 1C 1CA 2NL 1O
>
>
> PRES STNC 0.00 ! linkage for joining staple (atom names end in L)
> with backbone - post-staple
> ! 1 refers to previous (N terminal)
> ! 2 refers to next (C terminal)
> ! use in a patch statement
> DELETE IMPR 2N 1CL 2CA 2HN !Improper specified by IMPR N -C CA HN
> DELETE IC 1C 2CA *2N 2HN!Specified by IC -C CA *N HN
> BOND 1CL 2N
> IMPR 2N 1CL 2CA 2HN 1CL 1CAL 2N 1OL
>
> cheers,
> Doug
>
>
> Quoting Tristan Croll <tristan.croll_at_qut.edu.au> on Sat, 21 Jun 2014
> 23:43:43 +0000:
>
>> Let me see if I understand how you've put this together...
>>
>> You've got your special "linker" residue OL1 which is a 10-carbon chain
>> with a peptide backbone on each end, and a methyl group in place of the
>> alpha hydrogen. It's effectively symmetrical, but you've got one end
>> defined as the "backbone" and inserted as resid 3038, and are patching
>> the other end in between 3045 and 3047. So I take it...
>>
>> "patch DELB" deletes the existing amide bond between 3045 and 3047;
>> "patch STCN" makes a new amide bond between 3045 and 3038; patch STNC
>> makes the bond between 3038 and 3047... what does CMPS do?
>>
>> I'll let someone more knowledgeable than me comment on the behaviour
>> you're seeing... but may I suggest an easier way to get to the same end
>> goal? Why not chop your OL1 residue in half? Define it as simply a
>> (C-alpha) methylated amino acid with a linear 5-carbon sidechain, and
>> insert a copy at positions 3038 and 3046. Then it's one very simple
>> patch to link the two copies together at their terminal carbons. The
>> fewer (and simpler) patches you introduce, the less likely you are to
>> introduce problems - and those problems you do introduce will be easier
>> to troubleshoot.
>>
>>
>> Cheers,
>>
>> Tristan
>>
>> -----Original Message-----
>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
>> Behalf Of Douglas Houston
>> Sent: Friday, 20 June 2014 11:32 PM
>> To: Aron Broom
>> Cc: Namd Mailing List
>> Subject: Re: namd-l: Constraint failure in RATTLE algorithm
>>
>> Hi Aron,
>>
>> Thanks, this allows me to reproduce the problem. The following files
>> should be enough for anyone to visualise the instability:
>>
>> https://drive.google.com/file/d/0B3IbJv_UNHlWN3p0bTR6NjFER2M/edit?usp=sharing
>>
>> https://drive.google.com/file/d/0B3IbJv_UNHlWYXYwYkZCTmkzc2M/edit?usp=sharing
>>
>> https://drive.google.com/file/d/0B3IbJv_UNHlWQmlfTjhoNjZUZWc/edit?usp=sharing
>>
>>
>> Apart from the problem atoms flying around, I notice the whole system
>> is "pulsing" - is this normal or indicative of a problem with e.g.
>> pressure?
>>
>> cheres,
>> Doug
>>
>>
>> Quoting Aron Broom <broomsday_at_gmail.com> on Thu, 19 Jun 2014 11:37:59
>> -0400:
>>
>>> You'd just need to save that frame's coordinates using VMD, and then use
>>> those as an input for a "new" simulation. But of course don't do any
>>> minimization.
>>>
>>>
>>> On Thu, Jun 19, 2014 at 10:51 AM, Douglas Houston
>>> <DouglasR.Houston_at_ed.ac.uk
>>>> wrote:
>>>
>>>> Hi Aron,
>>>>
>>>> I had considered starting from just before where the distortion sets in
>>>> but wasn't sure how to do that?
>>>>
>>>> As I understand it the "firsttimestep" keyword doesn't specify the frame
>>>> to start on, merely where to start the numbering. Is there another
>>>> keyword
>>>> I need to use to get the simulation to start from a particular frame?
>>>>
>>>> cheers,
>>>> Doug
>>>>
>>>>
>>>>
>>>>
>>>> Quoting Aron Broom <broomsday_at_gmail.com> on Thu, 19 Jun 2014 10:15:49
>>>> -0400:
>>>>
>>>> You're right Normal, I did also mean DCDFreq.
>>>>>
>>>>> Douglas,
>>>>>
>>>>> What happens if you take your "penultimate frame" and restart from that,
>>>>> does it fail again very quickly?
>>>>>
>>>>> I agree that if it's taking any more than a few ps to crash,
>>>>> minimization
>>>>> likely isn't the problem. It sounds like there is a very sensitive
>>>>> problem
>>>>> that only appears under specific circumstances, maybe something with a
>>>>> dihedral.
>>>>>
>>>>> ~Aron
>>>>>
>>>>>
>>>>> On Thu, Jun 19, 2014 at 6:26 AM, Douglas Houston <
>>>>> DouglasR.Houston_at_ed.ac.uk>
>>>>> wrote:
>>>>>
>>>>> Hi all,
>>>>>>
>>>>>> Thanks for all the suggestions. A few more details:
>>>>>>
>>>>>> This is not particularly reproducible. The error may occur after 5ns or
>>>>>> 50ns. I have been running 20ns simulations and usually they finish, but
>>>>>> now
>>>>>> I want to do a 200ns simulation.
>>>>>>
>>>>>> When I visualise the trajectory just before the failure I see that the
>>>>>> residue the atom belongs to (3045) is heavily distorted in the final
>>>>>> frame;
>>>>>> it looks OK in the penultimate frame. I will rerun with smaller dcdfreq
>>>>>> as
>>>>>> Norman suggested. I will also increase the timestep from 0.5 to 2 fs as
>>>>>> this will hopefully throw the error sooner (my current simulation
>>>>>> failed
>>>>>> after 3 days of running).
>>>>>>
>>>>>> I do 10,000 minimization steps to start. The fact that the system is
>>>>>> stable for up to 50ns suggests to me that further initial minimization
>>>>>> won't help ... ?
>>>>>>
>>>>>> I understand that I may well have have a problem with bad
>>>>>> parameters, or
>>>>>> a
>>>>>> bad/incomplete topology. Residue 3045 has a number of patches
>>>>>> applied to
>>>>>> it.
>>>>>>
>>>>>> The following lists the psfgen commands I have been using to
>>>>>> generate the
>>>>>> topology:
>>>>>>
>>>>>> package require psfgen
>>>>>> topology top_all36_prot_ole.rtf
>>>>>> topology top_all36_lipid.rtf
>>>>>> topology toppar_water_ions.str
>>>>>> pdbalias residue HIS HSE
>>>>>> pdbalias atom ILE CD1 CD
>>>>>> segment A {pdb 5CstapleW2A.pdb
>>>>>> first ACE
>>>>>> last CT2}
>>>>>> patch DELB A:3045 A:3047
>>>>>> patch STCN A:3045 A:3038
>>>>>> patch STNC A:3038 A:3047
>>>>>> patch CMPS A:3045 A:3038 A:3047
>>>>>> coordpdb 5CstapleW2A.pdb A
>>>>>> regenerate angles dihedrals
>>>>>> guesscoord
>>>>>> writepdb 5CstapleW2A_psfgen.pdb
>>>>>> writepsf 5CstapleW2A_psfgen.psf
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Quoting Axel Kohlmeyer <akohlmey_at_gmail.com> on Wed, 18 Jun 2014
>>>>>> 14:23:05
>>>>>> -0400:
>>>>>>
>>>>>> On Wed, Jun 18, 2014 at 1:29 PM, Douglas Houston
>>>>>>
>>>>>>> <DouglasR.Houston_at_ed.ac.uk> wrote:
>>>>>>>
>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I keep encountering the following fatal error:
>>>>>>>>
>>>>>>>> ERROR: Constraint failure in RATTLE algorithm for atom 189!
>>>>>>>> ERROR: Constraint failure; simulation has become unstable.
>>>>>>>> ERROR: Exiting prematurely; see error messages above.
>>>>>>>>
>>>>>>>> The atom itself varies. I have searched previous messages and tried
>>>>>>>> the
>>>>>>>> suggestions (smaller timestep, minimization overkill, etc.) to no
>>>>>>>> avail.
>>>>>>>>
>>>>>>>> What else could I try to get my simulation to finish? I have attached
>>>>>>>> my
>>>>>>>>
>>>>>>>>
>>>>>>> you need to look at this from a different perspective. first you need
>>>>>>> to find out the reason, not try to suppress it.
>>>>>>>
>>>>>>> how reproducible is this failure? how soon does this happen after the
>>>>>>> start of your simulation. have you visualized your simulation around
>>>>>>> the time of the failure and seen where exactly an atom experiences
>>>>>>> (too) large forces. you may have a problem with bad parameters, or a
>>>>>>> bad/incomplete topology (= .psf) file. or you are very very far away
>>>>>>> from equilibrium and may need to do multiple iterations of
>>>>>>> minimization and relaxation. and so on and so on. there are many ways,
>>>>>>> but no simple general solution that works always.
>>>>>>>
>>>>>>> axel.
>>>>>>>
>>>>>>>
>>>>>>> .conf file so you can see my system and the simulation parameters I am
>>>>>>>
>>>>>>>> specifying.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> cheers,
>>>>>>>
>>>>>>>> Doug
>>>>>>>>
>>>>>>>> _____________________________________________________
>>>>>>>> Dr. Douglas R. Houston
>>>>>>>> Lecturer
>>>>>>>> Institute of Structural and Molecular Biology
>>>>>>>> Room 3.23, Michael Swann Building
>>>>>>>> King's Buildings
>>>>>>>> University of Edinburgh
>>>>>>>> Edinburgh, EH9 3JR, UK
>>>>>>>> Tel. 0131 650 7358
>>>>>>>> http://tinyurl.com/douglasrhouston
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>>>>>> College of Science & Technology, Temple University, Philadelphia
>>>>>>> PA, USA
>>>>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _____________________________________________________
>>>>>> Dr. Douglas R. Houston
>>>>>> Lecturer
>>>>>> Institute of Structural and Molecular Biology
>>>>>> Room 3.23, Michael Swann Building
>>>>>> King's Buildings
>>>>>> University of Edinburgh
>>>>>> Edinburgh, EH9 3JR, UK
>>>>>> Tel. 0131 650 7358
>>>>>> http://tinyurl.com/douglasrhouston
>>>>>>
>>>>>> --
>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>> Scotland, with registration number SC005336.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Aron Broom M.Sc
>>>>> PhD Student
>>>>> Department of Chemistry
>>>>> University of Waterloo
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> _____________________________________________________
>>>> Dr. Douglas R. Houston
>>>> Lecturer
>>>> Institute of Structural and Molecular Biology
>>>> Room 3.23, Michael Swann Building
>>>> King's Buildings
>>>> University of Edinburgh
>>>> Edinburgh, EH9 3JR, UK
>>>> Tel. 0131 650 7358
>>>> http://tinyurl.com/douglasrhouston
>>>>
>>>> --
>>>> The University of Edinburgh is a charitable body, registered in
>>>> Scotland, with registration number SC005336.
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>
>>
>>
>>
>> _____________________________________________________
>> Dr. Douglas R. Houston
>> Lecturer
>> Institute of Structural and Molecular Biology
>> Room 3.23, Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>> http://tinyurl.com/douglasrhouston
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
>>
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
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