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<DIV><FONT face=Arial size=2>Dear Users,</FONT></DIV>
<DIV><FONT face=Arial size=2> I am trying to simulate Drug –
Enzyme Complex accoring to "<FONT face=TimesNewRoman,Bold size=5><FONT
size=3>GROMACS Tutorial for Drug – Enzyme Complex" with different enzyme
(ALKALINE PHOSPHATASE FROM HUMAN PLACENTA - ZEF1) and ligand. After adding
water with genbox I run:</FONT></FONT></FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial size=2>grompp -f em.mdp -c trp_b4ion.pdb -p trp.top -o
trp_b4ion.tpr<BR></FONT></DIV>
<DIV><FONT face=Arial size=2>This is what I got:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>creating statusfile for 1 node...<BR>' for variable
integrator, using 'md'<BR>Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm'
'l-bfgs' 'tpi'<BR>' for variable ns-type, using 'Grid'<BR>Next time use one of:
'Grid' 'Simple'<BR>' for variable optimize_fft, using 'no'<BR>Next time use one
of: 'no' 'yes'<BR>' for variable constraints, using 'none'<BR>Next time use one
of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Back Off! I just backed up mdout.mdp to
./#mdout.mdp.2#<BR>checking input for internal consistency...<BR>calling
/usr/bin/cpp...<BR>processing topology...<BR>Generated 1284 of the 1485
non-bonded parameter combinations<BR>Excluding 3 bonded neighbours for Protein_A
1<BR>Excluding 3 bonded neighbours for Protein_B 1<BR>Excluding 3 bonded
neighbours for DRG 1<BR>Excluding 2 bonded neighbours for SOL 21179<BR>Excluding
2 bonded neighbours for SOL 1711<BR>NOTE:<BR> System has non-zero total
charge: -6.999996e+00</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>processing coordinates...<BR>double-checking input
for internal
consistency...<BR>-------------------------------------------------------<BR>Program
grompp, VERSION 3.3.1<BR>Source code file: grompp.c, line: 1109</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Fatal error:<BR>There were 4 error(s) processing
your
input<BR>-------------------------------------------------------</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>"Working in the Burger Kings, Spitting on your
Onion Rings" (Slim Shady) </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">I would
like to know what was wrong with the molecules, but there was absolutely no
indication of that. </SPAN><SPAN lang=EN-GB
style="mso-ansi-language: EN-GB"><?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">Could
anyone explain what this 'double-checking' means and how to get something
meaningful of it?</SPAN><SPAN lang=EN-GB
style="mso-ansi-language: EN-GB"><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">I have
also tried some Windows versions (3.2.1, 3.3). They have also failed, but were
able to go beyond this point. Maybe the problem is with Protein_B which consists
of Mg and Zn ions.</SPAN><SPAN lang=EN-GB
style="mso-ansi-language: EN-GB"><o:p></o:p></SPAN></P></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thank you in advance for your help.</FONT></DIV>
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