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<DIV><FONT face=Arial color=#000000 size=2>Dear all,</FONT></DIV>
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<DIV><FONT face=Arial size=2>I'm trying to study the interaction between NADH and a protein. And because the parameters for NADH have been developed in amber99 and amber94 force fields, so I just used the contributed parameter files for my simulation. The coordinates I got from docking results.</FONT></DIV>
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<DIV><FONT face=Arial size=2>I made my whole system, including the protein and ligand in amber, and generated, say complex.inpcrd and complex.prmtop. Then I used the distributed amb2gmx.pl distributed elsewhere to convert them into complex.gro and complex.top. It seems to be work well. But I'm not sure whether it is appropriate to do that because my system is very big (the protein with 5000 atoms and NADH 71 atoms, plus solvent). I notice that amb2gmx.pl was only tested for small molecules. </FONT></DIV>
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<DIV><FONT face=Arial size=2>One more thing, I tried to run the minimization but maybe there is very close contact between the ligand and the protein so the minimization failed. The close contact maybe due to the added hydrogen atoms by amber, which were trimed away upon docking. </FONT></DIV>
<DIV><FONT face=Arial size=2>Below is the error:</FONT></DIV>
<DIV><SPAN style="FONT-SIZE: 12pt; COLOR: red"><STRONG>Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ]</STRONG></SPAN><FONT color=red><SPAN style="FONT-WEIGHT: bold; COLOR: red"><BR><FONT face="Times New Roman">Please report this to the mailing list (</FONT></SPAN></FONT><A href="mailto:gmx-users@gromacs.org" target=_blank><FONT face="Times New Roman" color=red><SPAN style="COLOR: red"><STRONG>gmx-users@gromacs.org</STRONG></SPAN></FONT></A><FONT face="Times New Roman" color=red><SPAN style="COLOR: red"><STRONG>)</STRONG></SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2>Does the problem comes from close contact between NADH and the protein or anything else? If it the case, then what should I do, because I cannot arbitrarily re-position the ligand, can I?</FONT></DIV>
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<DIV><FONT face=Arial size=2>Is there anyone experienced in this problem, could you please give me some advice, I really appreciate.</FONT></DIV>
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<DIV><FONT face=Arial size=2>Best regards,</FONT></DIV>
<DIV><FONT face=Arial size=2>Tri.</FONT></DIV>
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