<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:10pt"><font size="2">I am replying to the Gromacs User's list rather than directly.<br><br>On </font><font style="font-family: times new roman,new york,times,serif;" face="Arial" size="2">Monday, January 30, 2012 12:38 AM, </font><font style="font-family: times new roman,new york,times,serif;" face="Arial" size="2">Tom <dnaafm@gmail.com></font><font size="2"> wrote:</font><br><font style="font-family: times new roman,new york,times,serif;" face="Arial" size="2"><br></font><div>> Thanks for answering me my question and thanks for the nice open </div>
<div>> source code program!</div>
<div>> I found out my prvious problem due to the problem of my *mol2 file.</div>
<div>> <br></div>
<div>> Can you help with two more doubts?</div>
<div>> <br></div>
<div>> 1) Can you provide a reference for me if I want to cite your work of</div>
<div>> topolbuild program?</div>
<div><br>I have not published anything regarding topolbuild. As noted in the source code<br>comments, when I wrote it, I borrowed heavily from other sources.<br><br></div>
<div>> 2) i am making a chemical structure, which contains 2 hydrocarbon (surgar ring) </div>
<div>> connected with 2 H2PO4-. I tired to use topolbuild and oplsaa forcefield. I noticed</div>
<div>> oplss only has forcefield and partial charges MeOPO3H and MeOPO3--, but there </div>
<div>> are no parameters available for H2PO4-. But the program of topolbuild works magically </div>
<div>> to assign the charges, by which<b> the overal is -2</b>, which is exactly equal to the real</div>
<div>> situation (the total charges of my *mol2 file is -2) although the type of P is P???</div>
<div><br>Something has bothered me about the *.mol2 file excerpt you pasted in your original<br>e-mail. It did not have correct Tripos atom types in the sixth column and totally lacked<br>the seventh, eighth, and ninth columns that contain the atom segment number, the<br>residue name, and the atom charge which should be 0.0 for a molecule with NO_CHARGE<br>specified in the file heading. I can only assume that what you pasted in your original<br>e-mail was not the file you actually used.<br><br>> I want to consult you what kind of algorithm that you used to assign the partial charges</div>
<div>> and make the total equal to the expected value?</div>
<div><br>The command you listed in your original e-mail would not assign charges, but would<br>
take the charges given in the *.mol2 file. For the excerpt of an *.mol2 that you pasted<br>in your original e-mail, these charges would be 0.0 because the heading read NO_CHARGE<br>If the -charge option is given in the command line, the charge for each atom type is<br>read from the parameters file for the selected force field found in the directory pointed<br>to by the -dir parameter. The charges in the paramters files for these atom types and<br>force fields were copied from gromacs force field files. This is not in any way a<br>sophisticated charge assignment.<br><br></div>
<div>> If you have time and want to look at my *mol file and the generated *top file, i can email</div>
<div>> to you. </div>
<div><br>I had been under the impression that you had pasted an excerpt from your actual *.mol2<br>file although I do not see how that file could have been accepted as a valid *.mol2 file<br>by topolbuild<br></div><br><br><div>-- <br></div><div>
Bruce D. Ray, Ph.D.</div><div>Associate Scientist</div><div>IUPUI
Physics Dept.</div><div>402 N. Blackford St.</div><div>Indianapolis, IN 46202-3273</div><div><br></div> </div></body></html>