Re: [AMBER] ATTN, need revision

From: He, Amy via AMBER <amber.ambermd.org>
Date: Wed, 30 Aug 2023 15:15:37 +0000

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<mailto: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 Wed Aug 30 2023 - 08:30:02 PDT
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