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_arasteh2...@yahoo.com>
To: Discussion list for GROMACS users <gmx-users@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 <p...@uab.edu>
To: Discussion list for GROMACS users <gmx-users@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...
--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
Shima Arasteh <shima_arasteh2...@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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