[gmx-users] mismatch in coordinate and topology
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 21 17:49:14 CEST 2011
Samrat Pal wrote:
> 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.
Regarding (2) and (3) - the output of the PRODRG server will likely give poor
results. See the paper linked from
> (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
A dodecahedral box is likely going to be more efficient, but this is not
relevant to the problem at hand.
> (6) Then I tried to create the em.tpr file from em.mdp file using grompp
> 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.
OK, so do any of your molecules consist of 31 atoms? Do you get any notes about
> 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?
Did you properly increment the number of atoms in the coordinate file after
adding your ligands?
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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