Re: C36 force field

From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Tue Dec 11 2018 - 11:21:24 CST

Dear Victor,

The instruction seems to be so much useful in solving my problem.
Thank you so much for your help.

--
Regards,
Ashkan Shekaari,
Ph.D Candidate in Solid State Physics,
K. N. Toosi University of Technology,
Tehran, Iran
----- Original Message -----
From: "victor" <victor2008_at_gmail.com>
To: "namd-l" <namd-l_at_ks.uiuc.edu>, "shekaari" <shekaari_at_email.kntu.ac.ir>
Sent: Tuesday, December 11, 2018 8:34:51 PM
Subject: Re: namd-l: C36 force field
Follow the instruction:
http://mackerell.umaryland.edu/~kenno/cgenff/program.php#namd
On Tue, Dec 11, 2018 at 11:55 AM João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:
>
> 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
>>>
>>> --
>>> This message has been scanned for viruses and dangerous content by
>>> KNTU Antispam System (E.F.A. Project), and is believed to be clean.
>>
>>
>>
>> --
>> ……………………………………………………...
>> 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

This archive was generated by hypermail 2.1.6 : Fri Dec 06 2019 - 23:20:17 CST