<div>Hi, </div>
<div>thanks for the reply. I have removed those two 0's from the "imp" part and now the grompp (of 3.3) is working. The modified ligand.itp is looks like this:</div>
<div><font face="courier new,monospace" size="1">3 1 4 13 2 35.3 334.8 35.3 334.8 ; imp C2* O2* C3* C1*</font></div>
<div><font face="courier new,monospace" size="1">4 3 5 11 2 35.3 334.8 35.3 334.8 ; imp C3* C2* O3* C4*</font></div>
<div><font face="courier new,monospace" size="1">....</font></div>
<div><font face="courier new,monospace" size="1">13 3 1 2 1 0.0 1.3 3 0.0 1.3 3 ; dih C1* C2* O2* H8L</font></div>
<div><font face="courier new,monospace" size="1">11 4 3 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C4* C3* C2* O2*</font></div>
<div><font face="courier new,monospace" size="1">....</font></div>
<div>I didn't do anything to the "dih" part. Is this correct, with two extra columns representing "multi" for "dih" (3's shown above)? </div>
<div> </div>
<div>Another question is related with this. For the old grompp of 3.2.1, it didn't give any warning about the extra "0"s for the impropers. Does this affect the original MD results by 3.2.1?</div>
<div> </div>
<div>Thank you. </div>
<div> </div>
<div>Lei Zhou</div>
<div>Columbia University, NY</div>
<div> </div>
<div><br> </div>
<div><span class="gmail_quote">On 10/16/05, <b class="gmail_sendername">David</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">On Sat, 2005-10-15 at 21:43 -0400, Lei Zhou wrote:<br>> Hi,<br>><br>> I am trying to use grompp in the recently released
3.3 to treat a<br>> system of protein and ligand. However, with the same itp files used in<br>> 3.2.1, there is error message saying that<br>> ERROR 2 [file "ligand.itp", line 185]:<br>> Too many parameters
<br>> ERROR 3 [file "ligand.itp", line 186]:<br>> Too many parameters<br>> ERROR 4 [file "ligand.itp", line 187]:<br>> Too many parameters<br>><br>> ...<br>><br>> I checked that line and it contains information for dihedrals (made by prodrg webserver)
<br>> [ dihedrals ]<br>> ; ai aj ak al fu c0, c1, m, ...<br>> 3 1 4 13 2 35.3 334.8 0 35.3 334.8 0 ; imp C2* O2* C3* C1*<br>><br>> 4 3 5 11 2 35.3 334.8 0
35.3 334.8 0 ; imp C3* C2* O3* C4*<br><br>There shouldn't be a zero in the parameter section. The new grompp may<br>be a bit stricter on checking the input. Impropers take two parameters<br>only (plus two for FEP).<br>
<br>><br>> Could you give me some suggestions? Thanks.<br>><br>> Lei Zhou<br>> Columbia University<br>> New York, NY<br>><br>><br>> _______________________________________________<br>> gmx-users mailing list
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