Dear Mark,<br><br>I have used following .top file.<br><br>; Include forcefield parameters<br>#include "ffG53a6.itp"<br>#include "drg.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>Protein_X 3<br>
<br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 NL 1 SER N 1 0.129 14.0067 ; qtot 0.129<br> 2 H 1 SER H1 1 0.248 1.008 ; qtot 0.377<br>
------<br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>; Strong position restraints for InflateGRO<br>#ifdef STRONG_POSRES<br>#include "strong_posre.itp"<br>
#endif<br><br>;Include ligand topology<br>;#include "drg.itp"<br><br><br>; Include water topology<br>#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>
; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein<br><br>
[ molecules ]<br>; Compound #mols<br>Protein_X 1<br>yoh 1<br><br>Thanking you in anticipation.<br><br><br>On 13/04/2010 1:49 PM, Jignesh Patel wrote:<br>
> Hello,<br>
><br>
> while I am running grompp command, I am getting following error.<br>
><br>
> Opening library file /usr/local/gromacs/share/<div id=":1bj" class="ii gt">gromacs/top/ff_dum.itp<br>
> Generated 837 of the 2346 non-bonded parameter combinations<br>
> -------------------------------------------------------<br>
> Program grompp, VERSION 4.0.5<br>
> Source code file: toppush.c, line: 947<br>
> Fatal error:<br>
> Atomtype OS not found<br>
><br>
> Can anyone help me to solve this problem?<br>
<br>
Yep, they can point out that atom type OS is not found. Since at this<br>
stage only you know about your topology and system preparation, and more<br>
particularly why you're trying to #include "ff_dum.itp", only you can<br>
reason why. Perhaps sharing some more detail will help...<br>
<br>
Mark</div><br clear="all"><br>-- <br>Best Wishes,<br>Jignesh Patel<br>Pharmacoinformatics,<br>NIPER<br>