Hi Hossein As Victor said, you have to create individual mapping file for each molecule. Also, note that when you use csg_map with --trj traj.trr option, by default, all the frames in traj.trr will be mapped and written to ouput file, i.e., --out cg.gro, resulting in very large gro file containing mapped CG coordinates of each frame in traj.trr. However, if your objective is just to create initial CG .gro file for coarse-graining, such as by IBI, I would suggest you use options "--nframes 1 --begin teq" so that csg_map would map only single frame from traj.trr at time teq, where teq is the time in ps at which it is safe to assume AA-MD trajectories are equilibrated.
Good luck Sikandar On Tue, May 21, 2013 at 6:10 AM, Victor Ruehle <[email protected]> wrote: > Dear Hossein, > > multiple molecules per xml is currfently not supported. Instead, put them > in separate xml files an specify both files when calling csg_map, i.e.: > csg_map --cg "mol1.xml;mol2.xml" .... > > Cheers, > Victor > > > > > 2013/5/21 Hossein Motevaselian <[email protected]> > >> Hi >> >> I am trying to prepare a mapping file for a mixture with two distinct >> molecules. However, when I use the command csg_map --top topol.tpr --trj >> traj.trr --cg mixture.xml --out cg.gro, >> only the molecule that comes first in the mixture.xml (which is attached >> to this post) will be mapped and for the other one I get the warning: >> "unknown molecule "SOL" with ..." >> Do I need to create separate mapping files and combine them or it can be >> done just by using unique "mixture.xml" file. I will appreciate it if you >> can help me with this. >> >> P.S. I am using the same molecule names as in my atomistic topology file >> >> Bests, >> Hossein >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/votca?hl=en. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
