From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 20 2017 - 08:33:41 CST
The C36 update for nucleic acids is supposed to be quite good (I can't
speak from experience though).
You almost certainly want par_all36_na.prm. I'm not 100% certain that VMD
has fully switched to C36 as the default force field, so be sure that you
are also building your system with c36 topology files (top_all36_na.rtf).
On Mon, Nov 20, 2017 at 6:32 AM, NEHİR NALINCI <nehirnalinci_at_iyte.edu.tr>
wrote:
> Hi again,
> I have one question, which parameter file is suitable for thymine?
> ------------------------------
> *From: *"Giacomo Fiorin" <giacomo.fiorin_at_gmail.com>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>, "NEHİR NALINCI" <
> nehirnalinci_at_iyte.edu.tr>
> *Cc: *"Brian Radak" <brian.radak_at_gmail.com>
> *Sent: *Thursday, November 16, 2017 3:19:04 PM
> *Subject: *Re: namd-l: missing parameters.
>
> The two files you mention are from two different versions of the CHARMM
> force field. You should not mix and match, because some parameters have
> changed and their occurrence in different files has been reorganized.
>
> You can always get an up-to-date version of the entire ff database from
> here:
> http://mackerell.umaryland.edu/charmm_ff.shtml
>
> On Thu, Nov 16, 2017 at 2:28 AM, NEHİR NALINCI <nehirnalinci_at_iyte.edu.tr>
> wrote:
>
>> I use CHARMM files from vmd plugins "par_all36_na.prm and
>> par_all27_prot_lipid_na.inp". I tried to do like tutorial files. When I
>> run the simulation, I get errors that 12 dihedral parameters are missed.
>> Thank you.
>>
>> ------------------------------
>> *From: *"Brian Radak" <brian.radak_at_gmail.com>
>> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>, "NEHİR NALINCI" <
>> nehirnalinci_at_iyte.edu.tr>
>> *Sent: *Wednesday, November 15, 2017 5:10:46 PM
>> *Subject: *Re: namd-l: missing parameters.
>>
>> This is likely a topology and parameter problem. What force field are you
>> using? What format? XPLOR? AMBER? How did you construct the system?
>>
>> On 11/15/2017 07:53 AM, NEHİR NALINCI wrote:
>>
>> Hİ everyone,
>>
>> I took single strand DNA which contains A, G, C, T from the protein data
>> bank, but I didn't run the my simulation, because some dihedral parameters
>> are missing in the parameter files such as " ON1 CN1 CN3T CN3 ". I tried
>> to add all paramater files to take care of these dihedrals. How can I solve
>> this problem?
>>
>> Thank you for interest.
>>
>>
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
>
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