AMBER: problem in writing

From: Gustavo Pierdominici Sottile <>
Date: Mon, 07 Feb 2005 16:59:49 -0300

    The problem I have is that when using SANDER the .out file is allways
empty. Perhaps I am doing something wrong but can not realize what. I will
explain from the beggining: I have the pdb, two .in files for non-standard
aminoacids and the frcmod file. Then I use tleap with the following
addatomtypes {{"CS" "C" "sp3"}}
   addatomtypes {{"HG" "H" "sp3"}}
   loadamberparams fcrmod.mad
   mad= loadpdb a.pdb
   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
   saveamberparm mad prmcrd.crd
Then I do sander -O -i -p -c prmcrd.crd -o din.out, and
the file looks like this:
   imin=0, irest=0, ntx=1, tempi=0.0,
   ntt=3, temp0=4.0, tautp=0.4,
   ntp=0, taup=2.0, nrespa=1,
   nstlim=40000, dt=0.001,
   ntwe=100, ntwx=100, ntpr=100,

There is something wrong in my and prmcrd.crd files because when
I use those file taken from the amber/test/val.... directory, there is no
I do not know what I am missing
Pd= If I try to make a minimization, the same things happend. No file is
Thanks in advanve

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Received on Mon Feb 07 2005 - 20:53:01 PST
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