Thank you Amy.
Yes, I am trying to parameterize a modified nucleotide with Fluorine in
an aromatic ring. I looked up all the possible parameter library files
like parm10.dat, gaff.dat, and gaff2.dat. But did not get the parameters
I needed. Is there any way I can find or calculate these parameters? I
came across one method of doing it by using ab initio calculations. But
I am not sure how to go about this. It will be highly appreciated if you
could provide suggestions and resources.
thank you in advance
regards,
Priyasha
On 2023-08-30 20:45, He, Amy wrote:
> Hi,
>
> This official tutorial provides instructions on dealing with "ATTN"
> remarks in parameter modification files generated from the main
> parameter database:
>
> https://ambermd.org/tutorials/basic/tutorial5/
>
> As described in the tutorial, the common solution is to find these
> parameters from an alternate parameter database of a more generalized
> force field, such as GAFF.
>
> Just one comment on the parameter file you showed:
>
> Were you possibly trying to parameterize some 5-fluoro / 5-hydroxy
> nucleotides? Most tutorials I know for nonstandard residue
> parameterization were intended for modified amino acids. But there
> might be more specialized force fields for modified nucleotides. I
> believe many experts on this server can help you.
>
> Bests,
>
> --
>
> Amy He
>
> Chemistry Graduate Teaching Assistant
>
> Hadad Research Group
>
> Ohio State University
>
> he.1768.osu.edu
>
> From: Priyasha Majee via AMBER <amber.ambermd.org>
> Date: Wednesday, August 30, 2023 at 7:09 AM
> To: Amber <amber.ambermd.org>
> Subject: [AMBER] ATTN, need revision
>
> Dear All,
>
> I am working with a non-standard residue. After RESP ESP charge
> derivation using RED server, i get frcmod.unkown with missing
> parameters. I used parmchk2 to find the missing parameters but some of
> these are showing ATTN, need revision. I know I have to manually add
> the
> missing parameters. But how do i do that? i went through previous
> messages on mailing list. Wolf2pack has been used. but i cant seem to
> find the website. Can someone please give inputs and suggestions ?
>
> remark goes like this
>
> ANGLE
> CM-CM-F 70.000 121.000 same as F -CA-CA, penalty score= 11.1
> C -CM-F 0.000 0.000 ATTN, need revision
>
> For another molecule too:
>
> remark line goes like this
>
> ANGLE
> CM-CM-CW 63.000 117.000 same as CA-CM-CM, penalty score= 0.9
> C -CM-CW 63.000 120.700 same as C -CM-CM, penalty score= 9.5
> CW-C*-HA 0.000 0.000 ATTN, need revision
> CB-OS-CW 0.000 0.000 ATTN, need revision
> C*-CW-CM 66.546 120.000 Calculated using CA-CA-CA, penalty
> score=160.6
> C*-CW-OS 0.000 0.000 ATTN, need revision
> C*-CB-CB 63.000 108.800 same as C*-CB-CN, penalty score= 0.2
> CB-C*-HA 0.000 0.000 ATTN, need revision
> CB-CB-OS 0.000 0.000 ATTN, need revision
> CA-CB-OS 0.000 0.000 ATTN, need revision
> CM-CW-OS 0.000 0.000 ATTN, need revision
>
> Thank you in advance
>
> Regards,
>
> Priyasha
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Received on Thu Aug 31 2023 - 01:30:02 PDT
