The group definition should be at the end of the file,
possibly preceded by an end-of-restraints section.
I would try a simple md at 10K w/ no restraints to see
if there is a problem with the system or just the complex
mdin. Also you could convert prmtop+inpcrd back to pdb
and view to make sure the structure was built correctly.
Bill
Bill told me to send him the mdin file and this is what it has:
group of rest
500.0
FIND
CA CT * *
SEARCH
RES 1 476
END
END
&cntrl
irest=0, ntx=1, tempi=0.0, nmropt=1, ntr=1,
ntt=1, tautp=2.5,ntb=0, cut=9.0, ivcap=0,
nstlim=42000, ntwe=0, ntwx=4200, ntwv=0, ntpr=100,
&end
&ewald
eedmeth=5,
&end
&wt
type="TEMP0", istep1=0, istep2=24000, value1=0.0, value2=300.0,
&end
&wt
type="TEMP0", istep2=24001, istep1=42000, value1=300.0, value2=300.0,
&end
&wt
type="END",
&end
If you think that the problem is the system and not the mdin file. The crd
input file was obtained with leap and this commands:
addatomtypes {{"CS" "C" "sp3"}}
addatomtypes {{"HG" "H" "sp3"}}
loadamberprep trp.in
loadamberprep trp1.in
loadamberparams fcrmod.mad
mad= loadpdb a.pdb
bond mad.146.SG mad.161.SG
bond mad.402.CE3 mad.453.CD1
bond mad.454.SG mad.423.SG
bond mad.422.SG mad.391.SG
bond mad.466.SG mad.381.SG
bond mad.383.SG mad.431.SG
bond mad.433.SG mad.368.SG
bond mad.374.SG mad.406.SG
solvateCap mad WATBOX216 mad.247.CD1 41.0 1.0
saveamberparm mad imp.top imp.crd
trp.in and trp1.in are two new aminoacids that I had to add, and HG and CS
are two new atom types that I need so as to modify manually the ACOEF of vdw
interaction of this two atoms, in the .top file
bond are made between CYX and another is for the interation between the new
aminoacids I have defined
Thanking in advance
Gustavo
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Received on Wed Mar 09 2005 - 15:53:00 PST
