Re: AMBER: vlimit in heating

From: Bill Ross <>
Date: Wed, 9 Mar 2005 07:44:06 -0800 (PST)

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 told me to send him the mdin file and this is what it has:
        group of rest
        CA CT * *
        RES 1 476
           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,
         type="TEMP0", istep1=0, istep2=24000, value1=0.0, value2=300.0,
         type="TEMP0", istep2=24001, istep1=42000, value1=300.0, value2=300.0,
        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"}}
           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.crd
        and 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
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Received on Wed Mar 09 2005 - 15:53:00 PST
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