AMBER Archive (2003)

Subject: Re: H-O-H angle

• Next message: tianxiao yang: "Sander help"
• Previous message: Ioana Cozmuta: "Re: Increase lastist in the &cntrl namelist"
• In reply to: Ioana Cozmuta: "H-O-H angle"
• Next in thread: Ioana Cozmuta: "Re: H-O-H angle"
• Reply: Ioana Cozmuta: "Re: H-O-H angle"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Hi Ioana,

I used recompiled the program without any problems after changing unit.c
and have been using namd out of the box. I also changed the leaprc in
order to load a modified WATBOX216:
------
#loadOff DAT/lib/solvents.lib
#HOH = TP3
#WAT = TP3

loadOff DAT/lib/tpl.lib
HOH = TPL
WAT = TPL
------

This loads tpl.lib with is a modification of the amber TIP3P water in
which the bond H-H is deleted. Here is the "not very smart" command file
to make this new lib:
-------
clearVariables
logFile tpl.log
#
# load water models
#

addAtomTypes {
         { "HY" "H" "sp3" }
         { "OY" "O" "sp3" }
}

#
# TIP3 water (shake on the angle)
#

h1 = createAtom H1 HY 0.417
h2 = createAtom H2 HY 0.417
o = createAtom O OY -0.834

set h1 element H
set h2 element H
set o element O

r = createResidue WAT
add r h1
add r h2
add r o

bond h1 o
bond h2 o

TPL = createUnit TPL

add TPL r
set TPL.1 restype solvent
set TPL.1 imagingAtom TPL.1.O

zMatrix TPL {
         { H1 O 0.9572 }
         { H2 O H1 0.9572 104.52 }
}

loadOff ./tip3pbox.off

TPLBOX216 = copy WATBOX216
deletebond TPLBOX216.1.2 TPLBOX216.1.3
deletebond TPLBOX216.2.2 TPLBOX216.2.3
deletebond TPLBOX216.3.2 TPLBOX216.3.3
deletebond TPLBOX216.4.2 TPLBOX216.4.3
deletebond TPLBOX216.5.2 TPLBOX216.5.3
deletebond TPLBOX216.6.2 TPLBOX216.6.3
deletebond TPLBOX216.7.2 TPLBOX216.7.3
deletebond TPLBOX216.8.2 TPLBOX216.8.3
deletebond TPLBOX216.9.2 TPLBOX216.9.3
deletebond TPLBOX216.10.2 TPLBOX216.10.3
deletebond TPLBOX216.11.2 TPLBOX216.11.3
deletebond TPLBOX216.12.2 TPLBOX216.12.3
deletebond TPLBOX216.13.2 TPLBOX216.13.3
deletebond TPLBOX216.14.2 TPLBOX216.14.3
deletebond TPLBOX216.15.2 TPLBOX216.15.3
deletebond TPLBOX216.16.2 TPLBOX216.16.3
deletebond TPLBOX216.17.2 TPLBOX216.17.3
deletebond TPLBOX216.18.2 TPLBOX216.18.3
deletebond TPLBOX216.19.2 TPLBOX216.19.3
deletebond TPLBOX216.20.2 TPLBOX216.20.3
deletebond TPLBOX216.21.2 TPLBOX216.21.3
deletebond TPLBOX216.22.2 TPLBOX216.22.3
deletebond TPLBOX216.23.2 TPLBOX216.23.3
deletebond TPLBOX216.24.2 TPLBOX216.24.3
deletebond TPLBOX216.25.2 TPLBOX216.25.3
deletebond TPLBOX216.26.2 TPLBOX216.26.3
deletebond TPLBOX216.27.2 TPLBOX216.27.3
deletebond TPLBOX216.28.2 TPLBOX216.28.3
deletebond TPLBOX216.29.2 TPLBOX216.29.3
deletebond TPLBOX216.30.2 TPLBOX216.30.3
deletebond TPLBOX216.31.2 TPLBOX216.31.3
deletebond TPLBOX216.32.2 TPLBOX216.32.3
deletebond TPLBOX216.33.2 TPLBOX216.33.3
deletebond TPLBOX216.34.2 TPLBOX216.34.3
deletebond TPLBOX216.35.2 TPLBOX216.35.3
deletebond TPLBOX216.36.2 TPLBOX216.36.3
deletebond TPLBOX216.37.2 TPLBOX216.37.3
deletebond TPLBOX216.38.2 TPLBOX216.38.3
deletebond TPLBOX216.39.2 TPLBOX216.39.3
deletebond TPLBOX216.40.2 TPLBOX216.40.3
deletebond TPLBOX216.41.2 TPLBOX216.41.3
deletebond TPLBOX216.42.2 TPLBOX216.42.3
deletebond TPLBOX216.43.2 TPLBOX216.43.3
deletebond TPLBOX216.44.2 TPLBOX216.44.3
deletebond TPLBOX216.45.2 TPLBOX216.45.3
deletebond TPLBOX216.46.2 TPLBOX216.46.3
deletebond TPLBOX216.47.2 TPLBOX216.47.3
deletebond TPLBOX216.48.2 TPLBOX216.48.3
deletebond TPLBOX216.49.2 TPLBOX216.49.3
deletebond TPLBOX216.50.2 TPLBOX216.50.3
deletebond TPLBOX216.51.2 TPLBOX216.51.3
deletebond TPLBOX216.52.2 TPLBOX216.52.3
deletebond TPLBOX216.53.2 TPLBOX216.53.3
deletebond TPLBOX216.54.2 TPLBOX216.54.3
deletebond TPLBOX216.55.2 TPLBOX216.55.3
deletebond TPLBOX216.56.2 TPLBOX216.56.3
deletebond TPLBOX216.57.2 TPLBOX216.57.3
deletebond TPLBOX216.58.2 TPLBOX216.58.3
deletebond TPLBOX216.59.2 TPLBOX216.59.3
deletebond TPLBOX216.60.2 TPLBOX216.60.3
deletebond TPLBOX216.61.2 TPLBOX216.61.3
deletebond TPLBOX216.62.2 TPLBOX216.62.3
deletebond TPLBOX216.63.2 TPLBOX216.63.3
deletebond TPLBOX216.64.2 TPLBOX216.64.3
deletebond TPLBOX216.65.2 TPLBOX216.65.3
deletebond TPLBOX216.66.2 TPLBOX216.66.3
deletebond TPLBOX216.67.2 TPLBOX216.67.3
deletebond TPLBOX216.68.2 TPLBOX216.68.3
deletebond TPLBOX216.69.2 TPLBOX216.69.3
deletebond TPLBOX216.70.2 TPLBOX216.70.3
deletebond TPLBOX216.71.2 TPLBOX216.71.3
deletebond TPLBOX216.72.2 TPLBOX216.72.3
deletebond TPLBOX216.73.2 TPLBOX216.73.3
deletebond TPLBOX216.74.2 TPLBOX216.74.3
deletebond TPLBOX216.75.2 TPLBOX216.75.3
deletebond TPLBOX216.76.2 TPLBOX216.76.3
deletebond TPLBOX216.77.2 TPLBOX216.77.3
deletebond TPLBOX216.78.2 TPLBOX216.78.3
deletebond TPLBOX216.79.2 TPLBOX216.79.3
deletebond TPLBOX216.80.2 TPLBOX216.80.3
deletebond TPLBOX216.81.2 TPLBOX216.81.3
deletebond TPLBOX216.82.2 TPLBOX216.82.3
deletebond TPLBOX216.83.2 TPLBOX216.83.3
deletebond TPLBOX216.84.2 TPLBOX216.84.3
deletebond TPLBOX216.85.2 TPLBOX216.85.3
deletebond TPLBOX216.86.2 TPLBOX216.86.3
deletebond TPLBOX216.87.2 TPLBOX216.87.3
deletebond TPLBOX216.88.2 TPLBOX216.88.3
deletebond TPLBOX216.89.2 TPLBOX216.89.3
deletebond TPLBOX216.90.2 TPLBOX216.90.3
deletebond TPLBOX216.91.2 TPLBOX216.91.3
deletebond TPLBOX216.92.2 TPLBOX216.92.3
deletebond TPLBOX216.93.2 TPLBOX216.93.3
deletebond TPLBOX216.94.2 TPLBOX216.94.3
deletebond TPLBOX216.95.2 TPLBOX216.95.3
deletebond TPLBOX216.96.2 TPLBOX216.96.3
deletebond TPLBOX216.97.2 TPLBOX216.97.3
deletebond TPLBOX216.98.2 TPLBOX216.98.3
deletebond TPLBOX216.99.2 TPLBOX216.99.3
deletebond TPLBOX216.100.2 TPLBOX216.100.3
deletebond TPLBOX216.101.2 TPLBOX216.101.3
deletebond TPLBOX216.102.2 TPLBOX216.102.3
deletebond TPLBOX216.103.2 TPLBOX216.103.3
deletebond TPLBOX216.104.2 TPLBOX216.104.3
deletebond TPLBOX216.105.2 TPLBOX216.105.3
deletebond TPLBOX216.106.2 TPLBOX216.106.3
deletebond TPLBOX216.107.2 TPLBOX216.107.3
deletebond TPLBOX216.108.2 TPLBOX216.108.3
deletebond TPLBOX216.109.2 TPLBOX216.109.3
deletebond TPLBOX216.110.2 TPLBOX216.110.3
deletebond TPLBOX216.111.2 TPLBOX216.111.3
deletebond TPLBOX216.112.2 TPLBOX216.112.3
deletebond TPLBOX216.113.2 TPLBOX216.113.3
deletebond TPLBOX216.114.2 TPLBOX216.114.3
deletebond TPLBOX216.115.2 TPLBOX216.115.3
deletebond TPLBOX216.116.2 TPLBOX216.116.3
deletebond TPLBOX216.117.2 TPLBOX216.117.3
deletebond TPLBOX216.118.2 TPLBOX216.118.3
deletebond TPLBOX216.119.2 TPLBOX216.119.3
deletebond TPLBOX216.120.2 TPLBOX216.120.3
deletebond TPLBOX216.121.2 TPLBOX216.121.3
deletebond TPLBOX216.122.2 TPLBOX216.122.3
deletebond TPLBOX216.123.2 TPLBOX216.123.3
deletebond TPLBOX216.124.2 TPLBOX216.124.3
deletebond TPLBOX216.125.2 TPLBOX216.125.3
deletebond TPLBOX216.126.2 TPLBOX216.126.3
deletebond TPLBOX216.127.2 TPLBOX216.127.3
deletebond TPLBOX216.128.2 TPLBOX216.128.3
deletebond TPLBOX216.129.2 TPLBOX216.129.3
deletebond TPLBOX216.130.2 TPLBOX216.130.3
deletebond TPLBOX216.131.2 TPLBOX216.131.3
deletebond TPLBOX216.132.2 TPLBOX216.132.3
deletebond TPLBOX216.133.2 TPLBOX216.133.3
deletebond TPLBOX216.134.2 TPLBOX216.134.3
deletebond TPLBOX216.135.2 TPLBOX216.135.3
deletebond TPLBOX216.136.2 TPLBOX216.136.3
deletebond TPLBOX216.137.2 TPLBOX216.137.3
deletebond TPLBOX216.138.2 TPLBOX216.138.3
deletebond TPLBOX216.139.2 TPLBOX216.139.3
deletebond TPLBOX216.140.2 TPLBOX216.140.3
deletebond TPLBOX216.141.2 TPLBOX216.141.3
deletebond TPLBOX216.142.2 TPLBOX216.142.3
deletebond TPLBOX216.143.2 TPLBOX216.143.3
deletebond TPLBOX216.144.2 TPLBOX216.144.3
deletebond TPLBOX216.145.2 TPLBOX216.145.3
deletebond TPLBOX216.146.2 TPLBOX216.146.3
deletebond TPLBOX216.147.2 TPLBOX216.147.3
deletebond TPLBOX216.148.2 TPLBOX216.148.3
deletebond TPLBOX216.149.2 TPLBOX216.149.3
deletebond TPLBOX216.150.2 TPLBOX216.150.3
deletebond TPLBOX216.151.2 TPLBOX216.151.3
deletebond TPLBOX216.152.2 TPLBOX216.152.3
deletebond TPLBOX216.153.2 TPLBOX216.153.3
deletebond TPLBOX216.154.2 TPLBOX216.154.3
deletebond TPLBOX216.155.2 TPLBOX216.155.3
deletebond TPLBOX216.156.2 TPLBOX216.156.3
deletebond TPLBOX216.157.2 TPLBOX216.157.3
deletebond TPLBOX216.158.2 TPLBOX216.158.3
deletebond TPLBOX216.159.2 TPLBOX216.159.3
deletebond TPLBOX216.160.2 TPLBOX216.160.3
deletebond TPLBOX216.161.2 TPLBOX216.161.3
deletebond TPLBOX216.162.2 TPLBOX216.162.3
deletebond TPLBOX216.163.2 TPLBOX216.163.3
deletebond TPLBOX216.164.2 TPLBOX216.164.3
deletebond TPLBOX216.165.2 TPLBOX216.165.3
deletebond TPLBOX216.166.2 TPLBOX216.166.3
deletebond TPLBOX216.167.2 TPLBOX216.167.3
deletebond TPLBOX216.168.2 TPLBOX216.168.3
deletebond TPLBOX216.169.2 TPLBOX216.169.3
deletebond TPLBOX216.170.2 TPLBOX216.170.3
deletebond TPLBOX216.171.2 TPLBOX216.171.3
deletebond TPLBOX216.172.2 TPLBOX216.172.3
deletebond TPLBOX216.173.2 TPLBOX216.173.3
deletebond TPLBOX216.174.2 TPLBOX216.174.3
deletebond TPLBOX216.175.2 TPLBOX216.175.3
deletebond TPLBOX216.176.2 TPLBOX216.176.3
deletebond TPLBOX216.177.2 TPLBOX216.177.3
deletebond TPLBOX216.178.2 TPLBOX216.178.3
deletebond TPLBOX216.179.2 TPLBOX216.179.3
deletebond TPLBOX216.180.2 TPLBOX216.180.3
deletebond TPLBOX216.181.2 TPLBOX216.181.3
deletebond TPLBOX216.182.2 TPLBOX216.182.3
deletebond TPLBOX216.183.2 TPLBOX216.183.3
deletebond TPLBOX216.184.2 TPLBOX216.184.3
deletebond TPLBOX216.185.2 TPLBOX216.185.3
deletebond TPLBOX216.186.2 TPLBOX216.186.3
deletebond TPLBOX216.187.2 TPLBOX216.187.3
deletebond TPLBOX216.188.2 TPLBOX216.188.3
deletebond TPLBOX216.189.2 TPLBOX216.189.3
deletebond TPLBOX216.190.2 TPLBOX216.190.3
deletebond TPLBOX216.191.2 TPLBOX216.191.3
deletebond TPLBOX216.192.2 TPLBOX216.192.3
deletebond TPLBOX216.193.2 TPLBOX216.193.3
deletebond TPLBOX216.194.2 TPLBOX216.194.3
deletebond TPLBOX216.195.2 TPLBOX216.195.3
deletebond TPLBOX216.196.2 TPLBOX216.196.3
deletebond TPLBOX216.197.2 TPLBOX216.197.3
deletebond TPLBOX216.198.2 TPLBOX216.198.3
deletebond TPLBOX216.199.2 TPLBOX216.199.3
deletebond TPLBOX216.200.2 TPLBOX216.200.3
deletebond TPLBOX216.201.2 TPLBOX216.201.3
deletebond TPLBOX216.202.2 TPLBOX216.202.3
deletebond TPLBOX216.203.2 TPLBOX216.203.3
deletebond TPLBOX216.204.2 TPLBOX216.204.3
deletebond TPLBOX216.205.2 TPLBOX216.205.3
deletebond TPLBOX216.206.2 TPLBOX216.206.3
deletebond TPLBOX216.207.2 TPLBOX216.207.3
deletebond TPLBOX216.208.2 TPLBOX216.208.3
deletebond TPLBOX216.209.2 TPLBOX216.209.3
deletebond TPLBOX216.210.2 TPLBOX216.210.3
deletebond TPLBOX216.211.2 TPLBOX216.211.3
deletebond TPLBOX216.212.2 TPLBOX216.212.3
deletebond TPLBOX216.213.2 TPLBOX216.213.3
deletebond TPLBOX216.214.2 TPLBOX216.214.3
deletebond TPLBOX216.215.2 TPLBOX216.215.3
deletebond TPLBOX216.216.2 TPLBOX216.216.3

a = { TPL TPLBOX216 }
saveOff a ./tpl.lib

quit
-------

I don't know if this is really necessary, but it works for me (also for
new prmtop).

Hope this helps,

best,

Luis

• Next message: tianxiao yang: "Sander help"
• Previous message: Ioana Cozmuta: "Re: Increase lastist in the &cntrl namelist"
• In reply to: Ioana Cozmuta: "H-O-H angle"
• Next in thread: Ioana Cozmuta: "Re: H-O-H angle"
• Reply: Ioana Cozmuta: "Re: H-O-H angle"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]