<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Problem solved, thanks a lot!<BR><BR><BR>
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<DIV class=plainMail><BR><BR>accomp lin wrote:<BR>> <<A href="http://www.mdbbs.org/tag-pull.html" target=_blank>http://www.mdbbs.org/tag-pull.html</A>><BR>> hi everyone,<BR>> <BR>> I;m using umbrella sampling to calculate PMF<BR>> <BR>> My system is DPPC + water + protein<BR>> In pull.ppa, I set runtype = umbrella ，reftype = com_t0，<BR>> K1 = 5000 ，Pos1 = 0.0 0.0 6.0<BR>> <BR>> However this came out when I finally type mdrun :<BR>> <BR>> Reading parameter file pull.ppa<BR>> ' for variable verbose, using 'no'<BR>> Next time use one of : 'no' 'yes'<BR>> ' for variable runtype, using 'afm'<BR>> Next time use one of : 'afm' 'constraint' 'umbrella'<BR>> ' for variable reftype, using 'com'<BR>> Next time use one of ; 'com' 'com_t0' 'dynamic' 'dynamic_t0'<BR>> .....................<BR>> .....................<BR>> .....................<BR>>
<BR><BR>Then something is badly formatted in the file. Perhaps it was edited on a Windows machine and has hidden formatting characters?<BR><BR>> ——————————————————————————————<BR>> program mdrun, VERSION 3.3.3<BR>> source code file: pullinit.c, line: 215<BR>> <BR>> Fatal error:<BR>> in the index fileGN<BR>> ——————————————————————————————<BR>> <BR>> It seems that mdrun doesn't recognize what I set in pull.ppa<BR>> And I don't know what's wrong with my index file, it looks all right to me.<BR>> So, can any body tell me what is going on?<BR><BR>Could also be related to the same formatting issues you're seeing with your .ppa file.<BR><BR>-Justin<BR><BR>> Thanks!<BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>>
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