[AMBER] error - binding_energy.mmpbsa run

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Sun, 16 May 2010 14:53:52 +0400

Dear Amber users, I have problems with binding energy calculation using binding_energy.mmpbsa. <br />The snapshots seem to be extracted correctly with the appriopriate names (2770 snapshots).<br /><br />"[voronkov.t60-2 PM-CAP-1IJYCAP]$ $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa &gt; binding_energy.log<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful<br />[voronkov.t60-2 PM-CAP-1IJYCAP]$&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful<br />"<br /><br />maybe I need to place these files sander_com.in -o sander_com.1.out locally, but I haven't found them in the tutorial?<br />The log is in the bottom, but seems not to be very informative, probably some problems with files names or command flags order?<br /><br />Sincerely yours,<br />Andrew<br /><br /><br />=&gt;&gt; Init data<br />&nbsp;&nbsp;&nbsp; Presuming executables of amber suite to be in /home/osolodkin/amber10/exe<br /><br />=&gt;&gt; Reading input parameters<br />&nbsp;&nbsp;&nbsp; Found PREFIX =&gt; snapshot<br />&nbsp;&nbsp;&nbsp; Found PATH =&gt; ./<br />&nbsp;&nbsp;&nbsp; Found COMPLEX =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found RECEPTOR =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found LIGAND =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found COMPT =&gt; ./1ijy-pmc_v.prmtop<br />&nbsp;&nbsp;&nbsp; Found RECPT =&gt; ./1ijy_v.prmtop<br />&nbsp;&nbsp;&nbsp; Found LIGPT =&gt; ./pmc_v.prmtop<br />&nbsp;&nbsp;&nbsp; Found GC =&gt; 0<br />&nbsp;&nbsp;&nbsp; Found AS =&gt; 0<br />&nbsp;&nbsp;&nbsp; Found DC =&gt; 0<br />&nbsp;&nbsp;&nbsp; Found MM =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found GB =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found PB =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found MS =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found NM =&gt; 0<br />&nbsp;&nbsp;&nbsp; Found PROC =&gt; 2<br />&nbsp;&nbsp;&nbsp; Found REFE =&gt; 0<br />&nbsp;&nbsp;&nbsp; Found INDI =&gt; 1.0<br />&nbsp;&nbsp;&nbsp; Found EXDI =&gt; 80.0<br />&nbsp;&nbsp;&nbsp; Found SCALE =&gt; 2<br />&nbsp;&nbsp;&nbsp; Found LINIT =&gt; 1000<br />&nbsp;&nbsp;&nbsp; Found PRBRAD =&gt; 1.4<br />&nbsp;&nbsp;&nbsp; Found ISTRNG =&gt; 0.0<br />&nbsp;&nbsp;&nbsp; Found RADIOPT =&gt; 0<br />&nbsp;&nbsp;&nbsp; Found NPOPT =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found CAVITY_SURFTEN =&gt; 0.0072<br />&nbsp;&nbsp;&nbsp; Found CAVITY_OFFSET =&gt; 0.00<br />&nbsp;&nbsp;&nbsp; Found SURFTEN =&gt; 0.0072<br />&nbsp;&nbsp;&nbsp; Found SURFOFF =&gt; 0.00<br />&nbsp;&nbsp;&nbsp; Found DIELC =&gt; 1.0<br />&nbsp;&nbsp;&nbsp; Found IGB =&gt; 2<br />&nbsp;&nbsp;&nbsp; Found GBSA =&gt; 1<br />&nbsp;&nbsp;&nbsp; Found SALTCON =&gt; 0.00<br />&nbsp;&nbsp;&nbsp; Found EXTDIEL =&gt; 80.0<br />&nbsp;&nbsp;&nbsp; Found INTDIEL =&gt; 1.0<br />&nbsp;&nbsp;&nbsp; Found SURFTEN =&gt; 0.0072<br />&nbsp;&nbsp;&nbsp; Found SURFOFF =&gt; 0.00<br />&nbsp;&nbsp;&nbsp; Found PROBE =&gt; 0.0<br /><br />=&gt;&gt; Checking sanity<br />&nbsp;&nbsp;&nbsp; Checking GENERAL<br />&nbsp;&nbsp;&nbsp; Setting START to default 1<br />&nbsp;&nbsp;&nbsp; Setting STOP to default 10e10<br />&nbsp;&nbsp;&nbsp; Setting OFFSET to default 1<br />&nbsp;&nbsp;&nbsp; Setting VERBOSE to default 0<br />&nbsp;&nbsp;&nbsp; Checking MM<br />&nbsp;&nbsp;&nbsp; Checking PB<br />&nbsp;&nbsp;&nbsp; Checking GB<br />&nbsp;&nbsp;&nbsp; Checking MS<br /><br />=&gt;&gt; Creating input<br />&nbsp;&nbsp;&nbsp; Sander input<br />&nbsp;&nbsp;&nbsp; PBSA input<br /><br />=&gt;&gt; Calculating energy / entropy contributions<br />&nbsp;&nbsp;&nbsp; Calc contrib for ./snapshot_com.crd.1<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Calc MM/GB/SAS<br />

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Received on Sun May 16 2010 - 04:00:03 PDT