From: Teerapong Pirojsirikul (tpirojsi_at_mail.ucsd.edu)
Date: Wed Sep 18 2013 - 15:45:54 CDT
Hi Kenno and Anna,
I'm not aware that Anna is working on a protein so sorry about that.
Personally, I am working on an RNA system. Anyway, I have 2 questions
here. 1) I don't think (but need your confirmation) that my modified
toppar_water_ions.str should cause any problem for systems with
regular nucleic acids, right? Those NBFIX terms I have commented out
have some thing to do with the interaction between Na ion and
carboxylate oxygens.
2) If I leave those NBFIX as is, I will get an error regarding unable
to find vdw parameter of OC atom type. My system itself has nothing to
do with this atom type and when I tried commenting those NBFIX lines
out, the problem solved. Is this because I haven't loaded what are
called 'the main files' before using the toppar_water_ions.str file?
And by that definition, what do those main files exactly mean?
Cheers,
Tee
2013/9/18 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>:
> Grace and Teerapong nailed it - you commented out the water parameter file,
> therefore NAMD complains it doesn't find the L-J parameters for water
> oxygen. Although this is pretty trivial, it is partially my fault because I
> suggested to use the file as downloaded from our site, while I should know
> that doesn't work with NAMD. The whole stroy is given below, but allow me to
> first warn you to !!! NOT USE TEERAPONG'S FILE !!! He or she commented out
> one NBFIX line too much, which will make any sodium ions in your solvent
> stick UNPHYSICALLY strongly to any carboxylate groups in your protein.
> Please read the explanation below. (I would also recommend the NAMD
> DEVELOPERS TO READ IT because it seems we have an unsolved problem on our
> hands that we didn't anticipate when releasing C36.) The short story is that
> the best thing you can do right now is to read *all* parameter files (even
> the ones you don't need) into NAMD, per the instructions on my home page:
> http://mackerell.umaryland.edu/~kenno/cgenff/program.html#namd
> Referring to these instructions, you do still need to comment out
> "parameters molecule.str", but nothing else.
>
> The whole story
> ===============
> There are 2 separate issues that prevent NAMD from reading
> toppar_water_ions.str . One is the CHARMM commands, the other is the NBFIX
> lines. Working around the former is relatively straightforward, but the
> latter isn't.
>
> The CHARMM commands
> -------------------
> These CHARMM commands were put into the file to work around a shortcoming in
> the CHARMM parameter reader. While this shortcoming is presumably fixed in
> the recent CHARMM 38 release (though I haven't confirmed this yet), the
> workaround will presumably remain in the file a while longer to support
> users of older CHARMM versions. As far as NAMD is concerned I see 2 possible
> workarounds:
> (1) Release separate versions of all the stream files that don't contain
> these commands
> (2) Make the NAMD parameter reader ignore everything outside of the
> parameter section (which starts with "read para" and ends with "end")
>
> The NBFIX lines
> ---------------
> These are actually pretty important, and cannot safely be removed. Their
> function is to work around an inherent problem with the Class I additive
> potential energy function (used in all major non-polarizable biomolecular
> force fields, not only CHARMM). Specifically, the CHARMM sodium and
> carboxylate nonbonded parameters were originally parameterized to interact
> correctly with water (which is very important), but it was found shortly
> afterwards that this *inherently* causes them to interact incorrectly with
> each other. NBFIX stands for "nonbonded fix", and fixes the
> sodium-carboxylate interaction. There are carboxylate groups with different
> oxygen atom types in the protein, lipid, carbohydrate and general force
> fields; that's why there are 4 NBFIX lines.
>
> The big problem is that if you haven't read the lipid force field into NAMD,
> it will choke on the lipid line; same thing for the other parts of the
> CHARMM force field. The CHARMM parameter reader also has this issue, but the
> BOMLEV and WRNLEV commands instruct it to ignore the unknown atom types. As
> far as NAMD is concerned, I see 3 possible workarounds:
> (1) Instruct all NAMD users to comment out *only* the lines associated with
> the parts of the force fields they're *not* using. This workaround is
> EXTREMELY DANGEROUS because even if all users manage to do the right thing
> when editing the file, users within the same lab will inevitably use each
> other's files for different simulations...
> (2) Instruct all NAMD users to ALWAYS read all 4 carboxylate-containing
> parameter files (protein, lipid, carbohydrate and general), even if such
> molecules aren't present in the simulation system. While this not a very
> clean thing to do, at least it's safe. Until a better solution is found, I
> changed the NAMD instructions on my home page this way:
> http://mackerell.umaryland.edu/~kenno/cgenff/program.html#namd
> (3) Make the NAMD parameter reader not bail out when finding unrecognized
> atom types in NBFIX lines (it would be even better to make it recognize the
> BOMLEV and WRNLEV commands, but this may be a bit too nontrivial to waste
> developer time on).
>
> Sorry for the wall of text but I feel it is really important that we (CHARMM
> and NAMD developers) find a solution to the NBFIX conundrum.
>
> Cheers,
>
> Kenno.
>
>
>
> On 09/18/2013 01:20 PM, Teerapong Pirojsirikul wrote:
>>
>> Hi,
>>
>> I saw you commented out toppar_water_ions.str which is required for
>> the OT atom type. It seems to me that OT atom type is for TIP3P
>> oxygen. My guess is you also used this file in psfgen and your system
>> is solvated with TIP3P water, right?. However, I found it's a little
>> bit tricky to also use this file in a namd configuratoin file. You
>> need to delete or comment out a bunch of lines in it. I'd recommend
>> trying my modified toppar_water_ions.mod.str attached. Just put it in
>> your working directory and fix the line
>>
>> paraTypeCharmm on
>> parameters ./par_all36_prot.prm
>> parameters ./par_all36_na.prm
>> #parameters ./toppar_water_ions.str
>>
>> to
>>
>> paraTypeCharmm on
>> parameters ./par_all36_prot.prm
>> parameters ./par_all36_na.prm
>> parameters ./toppar_water_ions.mod.str
>>
>> ,and give me feedback.
>>
>> Cheers,
>> Tee
>>
>>
>> 2013/9/18 Anna Chailyan <anna.chailyan_at_gmail.com>:
>>>
>>>
>>> Hello Hello!
>>>
>>> I am desperate !
>>>
>>> Today i made a new psf file with topology topology top_all36_prot.rtf and
>>> topology top_all36_na.rtf since my complex is made of protein and dna. It
>>> runs fine and i obtain the psf file.
>>> I attached the configuration file
>>>
>>> .
>>> It keeps crashing when i run minimization by saying "FATAL ERROR: DIDN'T
>>> FIND vdW PARAMETER FOR ATOM TYPE OT".
>>>
>>> I don't know, which are the possibilities.
>>>
>>>
>>>
>>> Best Regards,
>>>
>>>
>>> On Sep 18, 2013, at 1:20 AM, Kenno Vanommeslaeghe
>>> <kvanomme_at_rx.umaryland.edu> wrote:
>>>
>>> We recommend using the new CHARMM36 force field, which has significant
>>> improvements, and has been made modular (ie. no more need to merge
>>> parameter
>>> files). The force field can be downloaded from
>>> http://mackerell.umaryland.edu/CHARMM_ff_params.html
>>> Note that PSFs generated using the old force field usually won't work
>>> with
>>> the new one; one has to feed psfgen the new topology files from the force
>>> field distribution package. So assuming your system contains protein,
>>> lipids
>>> and water, Niklaus' recommendations for psfgen would become:
>>>
>>> topology top_all36_prot.rtf
>>> topology top_all36_lipid.rtf
>>> topology toppar_water_ions.str # not sure it will accept this
>>>
>>> and for NAMD:
>>>
>>> paraTypeCharmm on
>>> parameters par_all36_prot.prm
>>> parameters par_all36_lipid.prm
>>> parameters toppar_water_ions.str
>>>
>>> Cheers,
>>>
>>> Kenno.
>>>
>>> PS. For the record, the vintage *_all27_prot_lipids.* files were a merger
>>> of
>>> the CHARMM22 + CMAP protein force field and the CHARMM27 lipid force
>>> field,
>>> so the below methodology would have you read in obsolete CHARMM27 lipid
>>> definitions and parameters, then overwrite them with CHARMM36 ones. While
>>> I'm not sure this is a problem, it seems a bit risky.
>>>
>>>
>>>
>>> On 09/17/2013 12:35 PM, Niklaus Johner wrote:
>>>
>>> This looks like you didn't load the proper parameter files when running
>>> your simulations.
>>>
>>> Typically when you generate your psf with psfgen (I guess?), you input
>>> some topology files for example:
>>>
>>> topology top_all27_prot_lipids.rtf
>>> topology top_all36_lipid.rtf
>>>
>>> So then in your namd input you need to load the cognate parameter files.
>>> Something like:
>>>
>>> paraTypeCharmm on
>>> parameters par_all27_prot_lipids.prm
>>> parameters par_all36_lipid.prm
>>>
>>> Otherwise some of the atoms defined in your psf file won't be defined in
>>> the parameter files.
>>>
>>> N.
>>>
>>>
>>> Niklaus Johner
>>> Weill Cornell Medical College
>>> Harel Weinstein Lab
>>> Department of Physiology and Biophysics
>>> 1300 York Avenue, Room D-501
>>> New York, NY 10065
>>>
>>>
>>>
>>> On Sep 17, 2013, at 12:10 PM, Anna Chailyan wrote:
>>>
>>>
>>> Help!
>>>
>>> After all the previous successful steps finally i have psf file of my
>>> complex and now when i try to minimize it i get this message:
>>>
>>>
>>>
>>> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
>>>
>>> Charm++ fatal error:
>>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
>>>
>>>
>>> I am using NAMD_2.9_MacOSX-x86_64-multicore and i wonder why do i get
>>> this message now, not when i actually generated psf file.
>>> Please ! if there is someone that got this problem and knows how to
>>> solve it, share it with me!
>>> Best regards,
>>> Anna
>>>
>>>
>>>
>>>
>>>
>
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