<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:10pt"><div>On <font style="font-family: times new roman,new york,times,serif;" face="Arial" size="2">Friday, February 3, 2012 at 12:31 AM</font><span style="font-family: times new roman,new york,times,serif;">, </span><font style="font-family: times new roman,new york,times,serif;" face="Arial" size="2">Tom <dnaafm@gmail.com> wrote:</font><br></div>
<div> </div>
<div>> Any one has the experience of topolbuild?</div>
<div>> </div>
<div>> I tried to build *top file with the software of topolbuild</div>
<div>> <br></div>
<div>> ./topolbuild -n lipid -dir /home/computer/Tom/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff oplsaa</div>
<div>> <br></div>
<div>> I chose oplssaa. But from the generated *top file,<b> these charges in *top file can</b></div>
<div>> <b>not match the partial charges in file (in gromacs package) of </b></div>
<div>> /opt/gromacs-4.5.4/share/gromacs/top/oplsaa.ff/ffnonbonded.itp</div>
<div>> <br></div>
<div>> How to understand these charges on *top file, which topolbuild generates?</div>
<div>> Thanks for your instruction!</div>
<div> <br>First, topolbuild never "generates" charges. Unless the -charge option is specified,<br>the charges come from whatever is read as being the charge entry in the *.mol2 file.<br>If the charge type in the header of the *.mol2 file reads "INVALID", or "NO_CHARGE",<br>the charges are reset to 0 as the *.mol2 file is read. If the -charge option is given,<br>topolbuild assigns charges given in the "Atoms data" section of the force field<br>parameters file in the directory pointed to by the -dir entry according to assigned<br>atom type. In the case of oplsaa, the parameters file is ffoplsaa.dat, the column is<br>labeled charge, and the assignment is based on oplsaa atom type number. All of<br>this, of course, relies on the *.mol2 file being syntactically correct according to<br>the rules given by Tripos, Inc. Some programs that attempt to write *.mol2 files<br>fail to write complete Sybyl atom types. Others do
write complete atom types,<br>but sometimes have problems getting the atom type correct, most notably with<br>the guanidino carbon of arginine which is supposed to be C.cat<br><br>I hope this short note helps.<br></div><div> </div><div>--</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>