# Re: [AMBER] makeDIST_RST

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 4 Mar 2021 11:17:50 -0500

Hi,

This might not be exactly what you want, but cpptraj can generate
sander distance restraint syntax using Amber mask syntax via the 'rst'
command, e.g. to create a distance restraint between the atoms of
residues 1 and 12 in tz2.parm7:

parm test/tz2.parm7
rst :1 :12 r1 2 r2 3 r3 4 r4 5 rk2 5 rk3 5 out temp.rst

Contents of temp.rst:

&rst iat=-1,-1,0
r1=2.000000, r2=3.000000, r3=4.000000, r4=5.000000, rk2=5.000000,
rk3=5.000000,
IGR1(1)=1,IGR1(2)=2,IGR1(3)=3,IGR1(4)=4,IGR1(5)=5,IGR1(6)=6,IGR1(7)=7,IGR1(8)=8,IGR1(9)=9,IGR1(10)=10,IGR1(11)=11,IGR1(12)=12,IGR1(13)=13,
IGR2(1)=196,IGR2(2)=197,IGR2(3)=198,IGR2(4)=199,IGR2(5)=200,IGR2(6)=201,IGR2(7)=202,IGR2(8)=203,IGR2(9)=204,IGR2(10)=205,IGR2(11)=206,IGR2(12)=207,IGR2(13)=208,IGR2(14)=209,IGR2(15)=210,IGR2(16)=211,IGR2(17)=212,IGR2(18)=213,IGR2(19)=214,IGR2(20)=215,IGR2(21)=216,IGR2(22)=217,
nstep1=0, nstep2=0,
&end

-Dan

On Thu, Mar 4, 2021 at 12:04 AM Ming Tang <m21.tang.qut.edu.au> wrote:
>
> Dear Amber experts,
>
> In this tutorial(http://ambermd.org/tutorials/advanced/tutorial4/<http://ambermd.org/tutorials/advanced/tutorial4/>), makeDIST_RST can generate sander distance restraint format between two atoms with a 7 colomn input file. May I ask is there a similar script that can generate the sander format of distance restraint between the center of mass of two group of atoms (atoms in each group are from the same residue) automatically by providing similar input as 7col.dist except that 1 residue has a number of atoms in one row?
>
> Many thanks,
> Ming
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Received on Thu Mar 04 2021 - 08:30:02 PST
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