<div style="DIRECTION: ltr"><span class="q">Luciano Costa wrote:<br>> Hi Spoel,<br>><br>><br>> I have great admiration for your research and effort in the developement<br>> of gromacs. I have this how example and inspiration for my job. In the
<br>> last week I wrote ask all lists about an question involving structure<br>> factor. I believe that the people in the list, in general, it don't<br>> have pratice with structure factor. I have tried to use g_rdf program
<br>> for to analyse trajectory file with respect structure factor. The system<br>> simulated is constituted by polymers. I have a program that to do<br>> (calculate) structure factor of xyz trajectory file. I did a program
<br>> that convert *.trr file in *.xyz file, but I would like to obtain<br>> structure factor by g_rdf. Unfortunatelly, I had some problems with<br>> respect a " list (in the C source program) " of atom type. Look this:
<br>><br>> Fatal error:<br>><br>> Error: atom type (opls_557) not in list (18 types checked)!<br>><br>> In the font program have:<br><br></span></div>
<div style="DIRECTION: ltr">This is a bug/missing feature in the sense that there are GROMOS atom<br>types hardcoded in the program. I will have a look, but it should be<br>quite easy to fix for yourself if you update t_cmTAble all the way up in
<br>the file. If you look closely you'll see that all the H entries are<br>dientical etc. If you have other atom types then please try to find the<br>correspoonding scattering factors..<br> </div>
<div style="DIRECTION: ltr"><span class="q"><br>><br>> #################################<br>> int return_atom_type (char *type)<br>> {<br>> int i;<br>><br>> for (i = 0; (i < asize(CM_t)); i++)
<br>> if (!strcmp (type, CM_t[i].Label))<br>> return i;<br>> gmx_fatal(FARGS,"\nError: atom type (%s) not in list (%d types<br>> checked)!\n",<br>> type,i);<br>><br>> return 0;
<br>> }<br>> #################################<br>><br>> I think that it search a string that correspond to atom type in<br>> opls_XXX. When I had construct my input file and how the system wasn't<br>> protein or biomolecules, being polymers, I setted new opls_XXX.
<br>><br>> Well, I don't know what to do now, because *.gro and topol.top files are<br>> ok. MD simulation is ok.<br>><br>> Can you help me, please ?!<br>><br>><br>> Regards.<br>><br>> very very thanks and, more time, congratulations by your effort and work.
<br>><br>><br>><br>><br>><br>><br>> --<br>> ## Luciano Tavares da Costa ###<br>> Laboratory of Molecular Spectroscopy<br>> ## Zipe Code:05508-000 IQ-USP Brazil#<br>> ##################################
<br><br><br></span></div>
<div style="DIRECTION: ltr">--<br>David.<br>________________________________________________________________________<br> </div>
<div style="DIRECTION: ltr"><span class="sg">David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden
<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@gromacs.org">
spoel@gromacs.org</a> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
</span></div><br clear="all"><br>-- <br>## Luciano Tavares da Costa ###<br>----> Laboratory of Molecular Spectroscopy <----- #
<a href="http://lem.iq.usp.br">http://lem.iq.usp.br</a>; mailto: <a href="mailto:ltcnikit@gmail.com">ltcnikit@gmail.com</a> # ## Zipe Code:05508-000 IQ-USP Brazil ## ###########################################