AMBER Archive (2005)

Subject: Re: AMBER: vlimit in heating

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Mar 09 2005 - 09:44:06 CST


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
        
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu