Fwd: Re: Re: [AMBER] error - binding_energy.mmpbsa run

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Wed, 02 Jun 2010 17:15:56 +0400

Addtional data: sander_com.in file is listed below and binding_energy.mmpbsa is in the attachment.<br /><br />Sincerely yours,<br />Andrew<br /><br />File generated by mm_pbsa.pl. Using&nbsp; MM GB<br />&nbsp;&amp;cntrl<br />&nbsp; ntf&nbsp;&nbsp;&nbsp; = 1,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ntb&nbsp;&nbsp;&nbsp; = 0,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; dielc&nbsp; = 1.0,<br />&nbsp; idecomp= 0,<br />&nbsp; igb&nbsp;&nbsp;&nbsp; = 2,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; saltcon= 0.00,<br />&nbsp; offset = 0.09,<br />&nbsp; intdiel= 1.0,&nbsp;&nbsp;&nbsp;&nbsp; extdiel= 80.0,<br />&nbsp; gbsa&nbsp;&nbsp; = 0,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; surften= 1.0,<br />&nbsp; cut&nbsp;&nbsp;&nbsp; = 999.0,&nbsp;&nbsp; nsnb&nbsp;&nbsp; = 99999,<br />&nbsp; scnb&nbsp;&nbsp; = 2.0,&nbsp;&nbsp;&nbsp;&nbsp; scee&nbsp;&nbsp; = 1.2,<br />&nbsp; imin&nbsp;&nbsp; = 1,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; maxcyc = 1,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ncyc&nbsp;&nbsp; = 0,<br />&nbsp;&amp;end<br /><br />Sincerely yours,<br />Andrew<br /><br />-------- Пересылаемое сообщение --------<br /><br />18.05.10, 09:49, "Andrew Voronkov" &lt;drugdesign@yandex.ru&gt;:<br /><br /><br />Probably because I've use rich text formatting. I've use plain text now, so it shoul be readable now.<br /><br />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]$ $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa &gt; binding_energy.log<br /> /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful<br />[voronkov@t60-2 PM-CAP-1IJYCAP]$ /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 /> Presuming executables of amber suite to be in /home/osolodkin/amber10/exe<br /><br />=&gt;&gt; Reading input parameters<br /> Found PREFIX =&gt; snapshot<br /> Found PATH =&gt; ./<br /> Found COMPLEX =&gt; 1<br /> Found RECEPTOR =&gt; 1<br /> Found LIGAND =&gt; 1<br /> Found COMPT =&gt; ./1ijy-pmc_v.prmtop<br /> Found RECPT =&gt; ./1ijy_v.prmtop<br /> Found LIGPT =&gt; ./pmc_v.prmtop<br /> Found GC =&gt; 0<br /> Found AS =&gt; 0<br /> Found DC =&gt; 0<br /> Found MM =&gt; 1<br /> Found GB =&gt; 1<br /> Found PB =&gt; 1<br /> Found MS =&gt; 1<br /> Found NM =&gt; 0<br /> Found PROC =&gt; 2<br /> Found REFE =&gt; 0<br /> Found INDI =&gt; 1.0<br /> Found EXDI =&gt; 80.0<br /> Found SCALE =&gt; 2<br /> Found LINIT =&gt; 1000<br /> Found PRBRAD =&gt; 1.4<br /> Found ISTRNG =&gt; 0.0<br /> Found RADIOPT =&gt; 0<br /> Found NPOPT =&gt; 1<br /> Found CAVITY_SURFTEN =&gt; 0.0072<br /> Found CAVITY_OFFSET =&gt; 0.00<br /> Found SURFTEN =&gt; 0.0072<br /> Found SURFOFF =&gt; 0.00<br /> Found DIELC =&gt; 1.0<br /> Found IGB =&gt; 2<br /> Found GBSA =&gt; 1<br /> Found SALTCON =&gt; 0.00<br /> Found EXTDIEL =&gt; 80.0<br /> Found INTDIEL =&gt; 1.0<br /> Found SURFTEN =&gt; 0.0072<br /> Found SURFOFF =&gt; 0.00<br /> Found PROBE =&gt; 0.0<br /><br />=&gt;&gt; Checking sanity<br /> Checking GENERAL<br /> Setting START to default 1<br /> Setting STOP to default 10e10<br /> Setting OFFSET to default 1<br /> Setting VERBOSE to default 0<br /> Checking MM<br /> Checking PB<br /> Checking GB<br /> Checking MS<br /><br />=&gt;&gt; Creating input<br /> Sander input<br /> PBSA input<br /><br />=&gt;&gt; Calculating energy / entropy contributions<br /> Calc contrib for ./snapshot_com.crd.1<br /> Calc MM/GB/SAS<br /><br />16.05.10, 15:40, "Jason Swails" :<br /><br />&gt; Hello,<br />&gt; <br />&gt; All I got was garbled markup language. Can you re-send without it?<br />&gt; <br />&gt; All the best,<br />&gt; Jason<br />&gt; <br />&gt; On Sun, May 16, 2010 at 6:53 AM, Andrew Voronkov wrote:<br />&gt; <br />&gt; &gt; Dear Amber users, I have problems with binding energy calculation using<br />&gt; &gt; binding_energy.mmpbsa. The snapshots seem to be extracted correctly<br />&gt; &gt; with the appriopriate names (2770 snapshots)."[voronkov@t60-2PM-CAP-1IJYCAP]$ $AMBERHOME/exe/<br />&gt; &gt; mm_pbsa.pl binding_energy.mmpbsa &gt; binding_energy.log /&gt; <br />&gt; &gt; /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out<br />&gt; &gt; -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful /&gt;[voronkov@t60-2PM-CAP-1IJYCAP]$ <br />&gt; &gt; /home/osolodkin/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out<br />&gt; &gt; -c ./snapshot_com.crd.1 -p ./1ijy-pmc_v.prmtop not successful" /&gt;maybe I need to place these files sander_com.in -o<br />&gt; &gt; sander_com.1.out locally, but I haven't found them in the tutorial?The<br />&gt; &gt; log is in the bottom, but seems not to be very informative, probably some<br />&gt; &gt; problems with files names or command flags order?Sincerely<br />&gt; &gt; yours,Andrew=&gt;&gt; Init data /&gt; Presuming executables of amber suite to be in<br />&gt; &gt; /home/osolodkin/amber10/exe=&gt;&gt; Reading input parameters /&gt; Found PREFIX =&gt; snapshot <br />&gt; &gt; Found PATH =&gt; ./ Found COMPLEX =&gt; 1 /&gt; Found RECEPTOR =&gt; 1 Found<br />&gt; &gt; LIGAND =&gt; 1 Found COMPT =&gt;<br />&gt; &gt; ./1ijy-pmc_v.prmtop Found RECPT =&gt;<br />&gt; &gt; ./1ijy_v.prmtop Found LIGPT =&gt; ./pmc_v.prmtop /&gt; Found GC =&gt; 0 Found AS =&gt;<br />&gt; &gt; 0 Found DC =&gt; 0 Found MM<br />&gt; &gt; =&gt; 1 Found GB =&gt; 1 <br />&gt; &gt; Found PB =&gt; 1 Found MS =&gt; 1 /&gt; Found NM =&gt; 0 Found PROC<br />&gt; &gt; =&gt; 2 Found REFE =&gt; 0 <br />&gt; &gt; Found INDI =&gt; 1.0 Found EXDI =&gt; 80.0 /&gt; Found SCALE =&gt; 2 Found LINIT<br />&gt; &gt; =&gt; 1000 Found PRBRAD =&gt; 1.4 /&gt; Found ISTRNG =&gt; 0.0 Found<br />&gt; &gt; RADIOPT =&gt; 0 Found NPOPT =&gt; 1 /&gt; Found CAVITY_SURFTEN =&gt; 0.0072 /&gt; Found CAVITY_OFFSET =&gt; 0.00 <br />&gt; &gt; Found SURFTEN =&gt; 0.0072 Found SURFOFF =&gt;<br />&gt; &gt; 0.00 Found DIELC =&gt; 1.0 <br />&gt; &gt; Found IGB =&gt; 2 Found GBSA =&gt; 1 /&gt; Found SALTCON =&gt; 0.00 Found<br />&gt; &gt; EXTDIEL =&gt; 80.0 Found INTDIEL =&gt; 1.0 /&gt; Found SURFTEN =&gt; 0.0072 <br />&gt; &gt; Found SURFOFF =&gt; 0.00 Found PROBE =&gt; 0.0 /&gt;=&gt;&gt; Checking sanity Checking<br />&gt; &gt; GENERAL Setting START to default 1 /&gt; Setting STOP to default 10e10 <br />&gt; &gt; Setting OFFSET to default 1 Setting VERBOSE to<br />&gt; &gt; default 0 Checking MM <br />&gt; &gt; Checking PB Checking GB <br />&gt; &gt; Checking MS=&gt;&gt; Creating input <br />&gt; &gt; Sander input PBSA input=&gt;&gt;<br />&gt; &gt; Calculating energy / entropy contributions Calc<br />&gt; &gt; contrib for ./snapshot_com.crd.1 /&gt; Calc MM/GB/SAS<br />&gt; &gt; _______________________________________________<br />&gt; &gt; AMBER mailing list<br />&gt; &gt; AMBER@ambermd.org<br />&gt; &gt; http://lists.ambermd.org/mailman/listinfo/amber<br />&gt; &gt;<br />&gt; &gt;<br />&gt; <br />&gt; <br /><br />_______________________________________________<br />AMBER mailing list<br />AMBER@ambermd.org<br />http://lists.ambermd.org/mailman/listinfo/amber<br /><br /><br />-------- Завершение пересылаемого сообщения --------<br /><br />

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Received on Wed Jun 02 2010 - 06:30:07 PDT
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