2016-02-04 11:32 GMT-07:00 Aliireza Moradzadeh <[email protected]>: > Dear Users, > > I want to map an all-atom molecule to three beads, but my initial itp file > does not have residue name or id and even in case of similar id I have atoms > with same name, It has just one resname and resid. Furthermore, my molecule > have group like CH2 and C4H9 which again have been named similarly. See part > of itp to get what I mean > 1 NA 1 Im NA 1 > 2 NA 1 Im NA 2 > 3 CR 1 Im CR 3 > 4 HA 1 Im HA 3 > 5 CW 1 Im CW 4 > 6 HA 1 Im HA 4 > 7 CW 1 Im CW 5 > 8 HA 1 Im HA 5 > > 9 C1 1 Im C1 6 > 10 H1 1 Im H1 6 > 11 H1 1 Im H1 6 > 12 H1 1 Im H1 6 > > 13 C1 1 Im C1 7 > 14 H1 1 Im H1 7 > 15 H1 1 Im H1 7 > 16 C2 1 Im C2 8 > 17 HC 1 Im HC 8 > 18 HC 1 Im HC 8 > 19 CS 1 Im CS 9 > 20 HC 1 Im HC 9 > 21 HC 1 Im HC 9 > 22 CT 1 Im CT 10 > 23 HC 1 Im HC 10 > 24 HC 1 Im HC 10 > 25 HC 1 Im HC 10 > > (1-8) one bead > (9-12) one bead > (13-25) one bead > > I am not sure if votca can work correctly for this system because of atom > naming and resid. Am I right? is there anyway to rectify this error without > running simulation again. In the mapping file, you need to use an atom identifier of the type X:YY:ZZ, where X is the residue id, YY is the residue name and ZZZ is the atom name. If you don't have these is will become harder, you can use $ csg_dump --top FILE to see how VOTCA names the atoms internally. You may be lucky and the identifier may still be unique and hence usable.
> I am thinking of replacing itp file with a new file but I am not sure if it > is going to be effective on trr file. No, VOTCA only reads the position, velocities and force from the trr file, so you can use a different topology file with that trajectory as long as the number of atoms are the same. Christoph > > Thanks, > Alireza > > -- > 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 https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
