Dear All,
I'm trying to define a restraint on the distance between centres of
masses of two proteins.
My input file for MD is:
run MD at 300K
&cntrl
ntc=2, ntf=2,
cut=15.0, nrespa=2, igb=2, saltcon=0.2, gbsa=1,
ntpr=100, ntwx=500, ntave=500,
nstlim = 500000, dt=0.002,
ntt=1, tempi=300.0, temp0=300.0, tautp=2.0,
ntx=5, irest=1, ntb=0,
nscm = 1000,
nmropt=1,
/
&wt type='END' /
LISTOUT=REST.out
DISANG=RESTRAINT
and my original RESTRAINT file was:
#
# Definuje restraint na odleglosc pomiedzy sroedkami mas obu bialek
&rst
IAT = -1, -1,
IALTD=1, r2=10, r3=35, r4=60, rk2=0, rk3=1,
IRESID=1,
IGR1= 2, 3, 4, 5, 0,
GRNAM1(1)='CA', GRNAM1(2)='CA', GRNAM1(3)='N',GRNAM1(4)='N',
IGR2=1, 1, 1, 1, 0,
GRNAM2(1)='CA', GRNAM2(2)='CA', GRNAM2(3)='CA', GRNAM2(4)='CA',
IR6=0,
&end
This only works when IGR2 is always 1 and GRNAM2 is alwas 'CA'. When I try
to change it I get an error:
Error: Too many atom ranges need to be stored for center-of-mass distance
restraints. MAXGRP = 5. This needs to be increased.
I found a tutorial on the web
(
http://amber.ch.ic.ac.uk/tutorial/dna_NMR/nmr_dna_tutorial.htm)
but it dosn't work in my case - I got the same error message as above.
However, I got it working when I changed IRESID to 0 and put numbers of CA
atoms in IGR1 nad IGR2. However, I am not sure what it actually does and
why I couldn't get it run with IRESID=1.
Thank you in advance for any comments
marcin
Dr Marcin Krol
Zaklad Bioinformatyki Collegium Medicum UJ
Kopernika 7E
31-501 Krakow
tel/fax (012) 422-77-64
e-mail mykrol.cyf-kr.edu.pl
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue May 18 2004 - 18:53:00 PDT
