Ioannis Beis wrote:
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.
Get a count of the number of atoms using 'wc -l' and subtract three - that's how
many atoms you have. Enter that on line 2 of the .gro file to make it a
legitimate file. Then:
genconf -renumber
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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