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

From: Josh Berryman <the.real.josh.berryman.gmail.com>
Date: Thu, 6 Feb 2020 14:34:00 +0100

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 06 2020 - 06:00:03 PST
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