From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Nov 19 2012 - 23:45:27 CST
Who can say for sure? While I made a point of citing CMAP, maybe not everyone does. Email the authors if you want to know definitively.
On Nov 19, 2012, at 9:38 PM, Dr. Eddie wrote:
> Thanks JC. May I ask, then, if a publication says they have used Charmm22 should I assume that they have not used the cross-terms unless they specified they used the charmm22/cmap or charmm27?
> Thanks again,
> Eddie
>
>
> On Sun, Nov 18, 2012 at 2:41 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> This is the correct link: http://mackerell.umaryland.edu/CHARMM_ff_params.html
>
> Make sure to use MATCHING topology and parameter sets, i.e., don't build your PSF file with charmm27 and then run the simulation with charmm36.
>
>
> On Nov 18, 2012, at 10:20 AM, Dr. Eddie wrote:
>
>> Thanks, JC. So I take away that even if I am not using the Energy specifically (only the dynamics: distances, rmsd etc) I need the cross terms.
>>
>> When I run some models in namd I get errors like:
>> FATAL ERROR: UNABLE TO FIND CROSSTERM PARAMETERS FOR C N CP1 C N CP1 C NH1
>> (ATOMS 11 12 13 25 15 16 17 27)
>>
>>
>> A previous post to the list gave the following (now broken link): http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
>> as a way to update the cmap terms and thus correct the error. Where is the most up to date protein parameter file located so I can then correct the above problem (assuming that is the problem).
>>
>> Thank you very much for your help!!
>> Eddie
>>
>>
>> On Sat, Nov 17, 2012 at 4:24 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>> I looked into this today. Stefan is using an outdated version of the CHARMM topology and parameters that do not have CMAP. The problem arises because when Mutator rebuilds the PSF file, it uses a more up-to-date version of the topology that adds some crossterms. When Stefan goes to the run the simulation with the outdated parameter file, it naturally can't find the appropriate values for those crossterms.
>>
>> I will mention this to Stefan.
>>
>> On Nov 16, 2012, at 1:48 PM, JC Gumbart wrote:
>>
>>> This line, for example, in the log file begs to differ:
>>>
>>> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
>>>
>>> CMAP has been in NAMD for many years now. This may be (or have been?) a mutator specific issue. If so, someone should check more closely that the plugin isn't generating additional superfluous cross terms.
>>>
>>> On Nov 16, 2012, at 1:15 PM, Dr. Eddie wrote:
>>>
>>>> does namd use the cross-terms in the psf file for its calculations or is it ignored?
>>>>
>>>> Prof.
>>>> Stefan Franzen: claims it does not
>>>> http://www4.ncsu.edu/~franzen/public_html/CH795N/projects/DHP_MD.htm
>>>>
>>>> Anyone know for sure?
>>>> Thanks,
>>>> Eddie
>>>>
>>>
>>
>>
>>
>>
>> --
>> Eddie
>>
>
>
>
>
> --
> Eddie
>
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