Re: Fwd: regarding protein-dna complex simulation please reply.......

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Dec 23 2008 - 01:21:11 CST

Make sure you hit "reply all" when responding to a message on NAMD-L,
so that everyone can read and respond to the posts.

Your message below is not complete, so I can't guess what that
specific error is. However, I imagine one problem is that after you
apply the patches for your bases, you still need to run "regenerate
angles dihedrals" (or select the equivalent button in psfgen). This
was just covered recently on the list if you want to find out more info.

If that doesn't solve your problem, please let us (all of us!) know.

On Dec 22, 2008, at 7:42 PM, prasun kumar wrote:

> top_all27_prot_na.rtf and par_all27_prot_na.prm
> when i just went through the psf file generated,I found that the
> error I am getting is because of this file. actually the
> particular dihedral angle is mentioned here.
>
> after this I removed that dihedral angle and then again start
> solvating,this time I am getting error like:
> Dihedral angle is not matching some thing like this
>
> Is it necessary to have dihedral angle in a particular o
> On Tue, Dec 23, 2008 at 1:00 AM, JC Gumbart <gumbart_at_ks.uiuc.edu>
> wrote:
> What parameter file(s) are you using for the simulation?
>
>
> On Dec 22, 2008, at 9:44 AM, prasun kumar wrote:
>>
>>
>> Respected all
>>
>> I am trying to simulate a protein dna complex.For this I run a
>> separate simulation for protein and DNA(I know its not a right
>> method,but its a test only because i am a beginner).For protein
>> its running fine but for DNA I am getting error which is folowing:
>>
>> FATAL ERROR: CAN'T FIND DIHEDRAL PARAMETERS FOR HN8 CN8 CN7B NN3A
>>
>> then I enquired Inp file and prm file I found that there is not
>> such type of dihedrals forming I have used the patches DEO1 for
>> C,T and DEO2 for G,A and 3pho &5ter.Can any one suggest me where I
>> am going wrong?
>>
>> It will be very helpfulk for me
>> waiting for your suggestions
>> thanking you
>> prasun
>>
>>
>>
>>
>> --
>> PRASUN (ASHOKA)
>>
>>
>>
>> --
>> PRASUN (ASHOKA)
>
>
>
>
> --
> PRASUN (ASHOKA)

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