AMBER Archive (2008)

Subject: Re: AMBER: distance restraint between non-bonded molecules

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Thu Dec 18 2008 - 10:49:51 CST

Good morning Carlos,
I tried that yesterday. The minimization ran to completion, but the
distances after minimization were not close to what was specified in the
RST file.
i will give the details:
i started with a fixbond file
11 ASN ND2 142 DT O4 2.5
11 ASN ND2 143 DT O4 5.5
69 ASN ND2 121 DT O4 2.5
69 ASN ND2 122 DT O4 5.5
>makeDIST_RST -upb fixbond -pdb CEBP8.pdb -rst RST
this worked ok. I should mention that the pdb file about does not
contain Na+ and water, i added that later in xleap. i also tried to
create a pdb file from the prmtop and inpcrd files after adding ions and
solvent and created an RST2 file from that and it was identical to RST.
the RST file is
#
# 11 ASN ND2 142 DT O4 2.5
 &rst
  ixpk= 0, nxpk= 0, iat= -1,2838, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,

      rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
 igr1= 180, 181,
 &end
#
# 11 ASN ND2 143 DT O4 5.5
 &rst
  ixpk= 0, nxpk= 0, iat= -1,2870, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
 igr1= 180, 181,
 &end
#
# 69 ASN ND2 121 DT O4 2.5
 &rst
  ixpk= 0, nxpk= 0, iat= -1,2171, r1= 1.30, r2= 1.80, r3= 2.81, r4= 3.31,
 igr1=1179,1180,
 &end
#
# 69 ASN ND2 122 DT O4 5.5
 &rst
  ixpk= 0, nxpk= 0, iat= -1,2203, r1= 1.30, r2= 1.80, r3= 6.17, r4= 6.67,
 igr1=1179,1180,
 &end
It looks okay accept shouldn't r3 = 2.5 and 5.5 as specified in fixbond
file?

Then i ran the following minimization (similar to a DNA tutorial online)
CEBP8 minimization of 20,000 steps with bond restraint
&cntrl
  imin = 1,
  maxcyc = 2000,
  ncyc = 1000,
  ntpr = 200,
  ntb = 1,
  cut = 10,
  nmropt = 1,
  pencut = -0.001,
/

&wt type='REST', istep1=0,istep2=5000,value1=0.1,value2=4.0, /
&wt type='REST', istep1=5001,istep2=20000,value1=4.0,value2=4.0, /

&wt type='END' /
LISTOUT = POUT
DISANG = RST

the output did not contain any value next to restraint, i figured that
is because the atoms i specified are not connected

NSTEP ENERGY RMS GMAX NAME NUMBER
    200 -2.2828E+05 2.2054E+00 3.6591E+02 C 980

 BOND = 13434.2852 ANGLE = 526.7743 DIHED =
1966.1836
 VDWAALS = 22440.1597 EEL = -265383.7453 HBOND =
0.0000
 1-4 VDW = 640.7248 1-4 EEL = -1908.6934 RESTRAINT =
0.0000
 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================

at the end of the minimization, i created a pdb file from the prmtop and
rst files and i looked at the distance i specified they were 3.3, 3.7,
2.8, 5.3 as opposed to 2.5, 5.5, 2.5, 5.5 respectively.

Lastly, shouldn't any deviation (0.001) be printed in a POUT file? that
file was not created.

I hope there is a mistake that i made somewhere and this can work for me.

Thanks,
Taufik

Carlos Simmerling wrote:
> yes you can, with nmropt=1. why will that not work? I use it all the time.
>
>
> On Wed, Dec 17, 2008 at 7:13 PM, Taufik Al-Sarraj
> <taufik.alsarraj_at_utoronto.ca <mailto:taufik.alsarraj_at_utoronto.ca>> wrote:
>
> Hello,
> If i have two molecules that are capable of forming a H-bond. is
> it possible to place a restraint between the two atoms, even
> though there is no bond between them?
>
> in other words how can i bring two non-bonded molecules closer
> together using a distance between two specific atoms?
>
> I just realized that using nmropt = 1 is not going to work for me.
>
>
>
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