Hi Priyasha,
I’m interested in force field development but not very confident with DNA/RNA simulations. I’m sure there are many other experts on this list, please help us if you have any comments/suggestions..
Here are a few things I feel you might want to try:
1. Run parmchk2 with -p $AMBERHOME/dat/leap/parm/gaff2.dat option
Same as the last command in Section 3 from the tutorial: https://ambermd.org/tutorials/basic/tutorial5/
This allows parmchk2 to type your modified nucleotide with GAFF2 atom types, and find the equivalents in the GAFF2 force field to the parameters you need.
For example, CM-CM-F could be c -cc-f in GAFF2. (You don’t have to look it up yourself, parmchk2 will find the synonym for you!) The GAFF2-derived frcmod hopefully will have lower penalty score and fewer ATTN remarks.
2. Check out this frcmod file: $AMBERHOME/dat/leap/parm/all_modrna08.frcmod
This is a premade frcmod file for modified RNAs. You may or may not find what you need from this frcmod, but it might give you some idea on how you can fill in the missing parameters in different ways.
3. Parameter derivation using calculations with higher level of theory
Please consider the following tools that are native to Amber parameter refinement:
mdgx
https://ambermd.org/tutorials/advanced/tutorial32/index.php
parafit
http://ambermd.org/tutorials/advanced/tutorial23/
The common way to fine-tune the selected parameters is fitting to single-point energies of multiple conformers. I’m not very sure if it’s still worth doing if you’re aiming at angles.
Hope this is mildly helpful..
Bests,
From: Priyasha Majee <22d0186.iitb.ac.in>
Date: Thursday, August 31, 2023 at 4:16 AM
To: He, Amy <he.1768.buckeyemail.osu.edu>, Amber <amber.ambermd.org>
Subject: Re: [AMBER] ATTN, need revision
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.
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/<
https://urldefense.com/v3/__https:/ambermd.org/tutorials/basic/tutorial5/__;!!KGKeukY!y2k5832soIBHE3L52rpE8e4geSYL7dx4BaulXtdHB3fx6DgtPjaiBdemTazi0gyg8Kj2O5jUU6R4b-4DII3Zw1jMJ-s8YPA$>
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 Thu Aug 31 2023 - 08:00:02 PDT
