[gmx-users] Formyl parameters

[Shima Arasteh]

I have got the formyl parameters through swissparam site (http://swissparam.ch/ ) . Then I seperate the formyl from other residues. After it , I got the topology for this and then I included the .itp file in it . Now I' d like to know how can I become sure that the formyl group is applied in simulation? 


Cheers,
Shima



________________________________
 From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, May 9, 2012 8:37 AM
Subject: Re: [gmx-users] Formyl parameters
 

What do you mean? Am I supposed to use CGenFF to derive parameters?

Cheers,
Shima



________________________________
 From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, May 9, 2012 5:20 AM
Subject: Re: [gmx-users] Formyl parameters
 

Where does swissparam get its parameters for charmm? and does it use custom atomtypes for generic molecules? I have been using CGenFF-derived parameters for molecules that aren't in base c36 and I think it's working well for me...
-- 
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Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:
Dear gmx users,
>
>
>My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I  got its .itp file through swissparam. Now I want to use its parametrs. As I read in gromacs.org ,  I need to include this .itp in .top file. How does it come when I have not got any .top file yet?
>Anybody can suggest me how I can use .itp file and solve my problem?
>
>
>Thanks in advance,
>Shima
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