Re: [AMBER] Shaw DE RNA ff in Amber format

From: Cavender, Chapin <Chapin_Cavender.URMC.Rochester.edu>
Date: Thu, 6 Feb 2020 21:23:53 +0000

> Hi Amir, I wrote a script that calls parmed to convert an existing amber
> topology to have the DES partial charges etc.

As far as I can tell, this script will update the nonbonded parameters but not the torsions, of which Tan et al. changed gamma, zeta, and chi for each nucleobase. Thus, it is an incomplete implementation of the DES RNA force field.

A full implementation of this force field is included in the supporting information of this publication: https://pubs.acs.org/doi/10.1021/acs.jctc.8b00955

Note that it is required to use both the TIP4P-D water model (Amber file included in the above publication) and the CHARMM22 parameters for monovalent ions (not included in the above publication) in order to match the conditions used in Tan et al. (2018). Here is an Amber frcmod file for the CHARMM22 parameters for Na+, K+, Cl-, and Mg2+:

Ion parameters from CHARMM22
MASS
Na+ 22.99 0.250 sodium pol: J. Phys. Chem. 11,1541,(1978)
K+ 39.10 1.060 potassium
Cl- 35.45 1.910 chlorine (Applequist)
Mg2+ 24.305
 
NONBON
  Na+ 1.36375 0.0469
  K+ 1.76375 0.0870
  Cl- 2.27 0.150
  Mg2+ 1.18500 0.0150

Best,
Chapin Cavender
PhD student, Dave Mathews lab
Department of Biochemistry & Biophysics
University of Rochester School of Medicine & Dentistry
________________________________________

Date: Thu, 6 Feb 2020 14:34:00 +0100
From: Josh Berryman <the.real.josh.berryman.gmail.com>
Subject: Re: [AMBER] Shaw DE RNA ff in Amber format
To: AMBER Mailing List <amber.ambermd.org>, amirhossein taghavi
        <taghavi.amirhossein.gmail.com>
Message-ID:
        <CANRE9HVz7P8YL2B3eOUXG72-cj7dcDwCY8WczbTy-heNZ6GvHQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi Amir, I wrote a script that calls parmed to convert an existing amber
topology to have the DES partial charges etc.

I'll paste it below
#############################
#!/bin/bash

inParm=$1
if [ -s "$inParm" ]
then
   echo "reading paramset from $inParm"
else
   echo "require input parm: .${inParm}. is not present"
   exit 1
fi

rm -f setDES.prmed

###define a pattern for charge modifications
chrg_pattern="BASE ATOM FF14 NEW"
declare -a cplist=(
"DC N4 -0.9530 -0.8716"
"DC H41 +0.4234 +0.3827"
"DC H42 +0.4234 +0.3827"
"DT N3 -0.3549 -0.3913"
"DT H3 +0.3154 +0.3518"
"DG N1 -0.4787 -0.5606"
"DG H1 +0.3424 +0.4243"
"DG N2 -0.9672 -1.0158"
"DG H21 +0.4364 +0.4607"
"DG H22 +0.4364 +0.4607"
"DA N1 -0.7615 -0.7969"
"DA H2 +0.0473 +0.0650"
"DA N6 -0.9019 -1.0088"
"DA H61 +0.4115 +0.4738"
"DA H62 +0.4115 +0.4738"
)
n_cp=${#cplist[.]}
for i in `seq 0 $[n_cp - 1]`
do
   pattern=${cplist[$i]}
   echo "applying charge pattern $i: $pattern"
   echo $pattern |\
       awk '{printf("printDetails :%s*.%s\n",$1,$2);\
             printf("change CHARGE :%s*.%s %s\n",$1,$2,$4)}' >> setDES.prmed
done
vdw_pattern="at_type sigma_old sigma_new eps_old eps_new master_mask"
declare -a vdwlist=(
"H 1.0691 0.0000 0.0157 0.0000
(:DG=.H1,H21,H22)|(:DA=.H61,H62)|(:DC=.H41,H42)|(:DT=.H3)"
"NA 3.2500 3.2890 0.1700 0.1700 (:DG=.N7,N9)|(:DA=.N1,N3,N7,N9)"
"NN 3.2500 3.3507 0.1700 0.1700
(:DG=.N1,N2,N3)|(:DA=.N6)|(:DT=.N1,N3)|(:DC=.N1,N3,N4)"
"CA 3.3997 3.3004 0.0860 0.0636 (:DA=.C2,C4,C5,C6,C8)"
"CN 3.3997 3.2850 0.0860 0.0538
(:DG=.C2,C4,C6,C6,C8)|(:DC=.C2,C4,C5,C6)|(:DT=.C2,C4,C5,C6)"
)

##new name _ residue _ list of old names
declare -a atname_matches=(
"NN DG* .N1 @N2 @N3"
"CN DG* .C2 @C4 @C5 @C6 @C8"
"NA DG* .N7 @N9"
"H DG* .H1 @H21 @H22"
"NA DA* .N1 @N3 @N7 @N9"
"NN DA* .N6"
"CA DA* .C2 @C4 @C5 @C6 @C8"
"H DA* .H61 @H62"
"NN DC* .N1 @N3 @N4"
"CN DC* .C2 @C4 @C5 @C6"
"H DC* .H41 @H42"
"NN DT* .N1 @N3"
"CN DT* .C2 @C4 @C5 @C6"
"NN DT* .N1 @N3"
"H DT* .H3"
)


n_vd=${#vdwlist[.]}
n_atpats=${#atname_matches[.]}
for i in `seq 0 $[n_vd - 1]`
do
   pattern=${vdwlist[$i]}
   echo "applying vdw pattern $i: $pattern"
   newAtName=$(echo $pattern | awk '{print $1}')
   regexp=$(echo $pattern | awk '{print $NF}')
   ##parmed takes Rmin as input.
   ##the paper gives sigma: not the same.
   radius=$(echo $pattern | awk '{print 0.5*(2**(1./6.))*$3}')
   epsilon=$(echo $pattern | awk '{print $5}')
   echo "printLJMatrix 1" >> setDES.prmed
   echo "printDetails $regexp" >> setDES.prmed

   echo "addLJType $regexp radius $radius epsilon $epsilon" >> setDES.prmed
   echo "printDetails $regexp" >> setDES.prmed
   echo "printLJMatrix 1" >> setDES.prmed
done
echo "parmout $1.des" >> setDES.prmed

rm -f $1.des
parmed $1 < setDES.prmed




On Thu, 23 Jan 2020 at 23:00, amirhossein taghavi <
taghavi.amirhossein.gmail.com> wrote:

> Hello all,
>
> Does anyone have the DE Shaw ff for RNA in Amber format:
>
> Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1346-E1355.
> "RNA force field with accuracy comparable to state-of-the-art protein orce
> fields." Tan D, Piana S, Dirks RM, Shaw DE.
>
> I saw Prof. Case asked this on Amber-developers but can not find any
> answer.
>
> Thanks in forward.
> Cheers,
> Amir
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Received on Thu Feb 06 2020 - 13:30:02 PST
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