[gmx-users] How to make coordinate file with correct numbering in the atoms when inbetween atoms are removed

[Ioannis Beis]

Dear gromacs users,

It seems that because of my inexperience I have been trapped in a  
simple-looking labyrinth. I wanted to change a .gro file containing  
hydrated bilayer, in which I want to remove/modify certain atoms from  
certain lipid residues, e.g. cutting off a polar head. This kind of  
structure would serve as starting structure subject to equilibration.  
Since the resulting structures -after deleting certain atom lines- had  
atoms missing, the numbering in the .gro file was no longer correct. I  
tried using trjconv and trjcat to solve the problem and they were  
complaining about the inconsistency between total number of atoms and  
numbering. pdb2gmx was complaining about not finding my residues in  
the files of the forcefield, even though I explicitly gave as an input  
my topology.

I supposed that I could do the job in matlab. I wrote a script for the  
simplest case, which made the appropriate operations and saved the  
file exactly in the same format. Nevertheless, vmd could not visualize  
the file at all, even though grompp could use it as an input to  
assemble the binary .tpr . I tried fromdos with the .gro file but had  
no result. I also tried using trjconv on the "invisible" file with  
additional input the .tpr file that I made earlier and this produced a  
new .gro file with modified names for lipid residues (e.g. 1DOPC  
instead of first four digits of the name 1DOP as it was in the  
original file), but made the file visible by vmd. Nonetheless, vmd  
interpreted my modified lipid into two residues, i.e. one polar  
hydrogen as one and the rest lipid as another (??), despite the fact  
that the .gro file has the correct numbering of residues.

I know that some of the above problems might be independent, but all I  
am looking for eventually is if there is a practical implementation of  
typing five words and a program from the GROMACS package taking the n  
atoms of the .gro file and correcting their number ID into the correct  
one, based on the order they appear in the file, so that they become  
1,2,...,n without gaps.

Thank you in advance.

Best regards,
Ioannis