[gmx-users] mismatch in coordinate and topology

Samrat Pal psamrat10 at yahoo.com
Fri Oct 21 17:05:16 CEST 2011

Hi All,
          I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it.
Following are the steps that I performed ----
(1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field 
(2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen 
a) no chirality, b) full charge and (c) no minimization. I have not seen any option for choosing force-field in the server.  
(3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after "posre.itp" and before "spc.itp"accordingly.
(4) I have also added two lines in the [molecules] section like, 
FAD  1
MHF  1
(5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox.
(6) Then I tried to create the em.tpr file from em.mdp file using grompp command.
I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message.
I have checked the topology file after solvation and it is updated having the last line of the file with SOL  34741.
I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? 
thanks in advance
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111021/757e28a0/attachment.html>

More information about the gromacs.org_gmx-users mailing list