Re: C36 force field

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Dec 11 2018 - 10:55:00 CST

Dear Ashkan,

Please keep namd-l_at_ks.uiuc.edu in the CC list so we can keep track of the
discussion and others can benefit from it as well.

if the simulation works fine using a parameter file from a previous CHARMM
version is because you are probably mixing topologies from different CHARMM
versions in the structure preparation phase, *which you should not do*.
You should consistently use the same CHARMM ff version during preparation
and run phases. I would suggest CHARMM36.

Best

João

On Tue, Dec 11, 2018 at 10:32 AM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
wrote:

> Dear João,
>
> Thank you so much for your help. I can now generate the psf file using
> multiple topology files.
> However, in minimization or equilibration processes, despite using the
> feature of importing several parameter files in .conf file as below:
>
> # FORCE-FIELD PARAMETERS
> ##
> ########################################################
> parameters ../solvation/par_all36_prot.prm
> parameters ../solvation/par_all36_lipid.prm
> parameters ../solvation/par_all36_na.prm
>
> I get the error message stating that
>
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB.
>
> This is while importing
>
> parameters ../solvation/par_all27_prot_lipid_na.inp
>
> works. That is why I am looking for a single file containing prot, lipid,
> and na
> just like par_all27_prot_lipid_na.inp prepared in NAMD tutorial files.
>
> --
> Best regards,
> Ashkan Shekaari,
> Ph.D Candidate in Solid State Physics,
> K. N. Toosi University of Technology,
> Tehran, Iran
>
> ------------------------------
> *From: *"João Ribeiro" <jribeiro_at_ks.uiuc.edu>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>, "shekaari" <shekaari_at_email.kntu.ac.ir
> >
> *Sent: *Tuesday, December 11, 2018 6:53:31 PM
> *Subject: *Re: namd-l: C36 force field
>
> Dear Ashkan,
>
> you might be getting confused about what you can and can't do. In your
> psfgen script, you can load more that one topology (or stream file) when
> building your structure. Just repeat the command "topology
> <topology/stream file>", like
>
> "
> ...
> topology top_all36_lipid.rtf
> topology top_all36_prot.rtf
> ...
> "
>
> You will only need the parameters to actually run the simulation.
>
> I hope this helps
>
> Best
>
> João
>
> On Tue, Dec 11, 2018 at 7:39 AM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
> wrote:
>
>> Dear experts,
>>
>> Is there any CHARMM36 all-hydrogen parameter file for both proteins and
>> lipids written in a single file?
>>
>> For prot, lipid, and na, there are three separate files, and therefore, I
>> cannot generate the psf file of my protein.
>>
>> --
>> Regards,
>> Ashkan Shekaari,
>> Ph.D Candidate in Solid State Physics,
>> K. N. Toosi University of Technology,
>> Tehran, Iran
>>
>> --
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>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851

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