Re: cross terms

From: Dr. Eddie (eackad_at_gmail.com)
Date: Mon Nov 19 2012 - 21:38:38 CST

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 Stefan is using an outdated version of the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 run the simulation with the outdated parameter file, it naturally can't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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