AMBER Archive (2005)

Subject: AMBER: vlimit in heating

From: Gustavo Pierdominici Sottile (gsottile_at_unq.edu.ar)
Date: Wed Mar 09 2005 - 08:13:20 CST

Hi , I have written because as soon as I have started the heating, the
problem of the vlimit appeared.
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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