[gmx-users] pdb2gmx -chainsep vs -merge

[Mark Abraham]

----- Original Message -----
From: nahren manuel <meetnahren at yahoo.com>
Date: Tuesday, September 7, 2010 20:33
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

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| > Dear Gromacs Users,
> 
> Tsjerk, 
> 
> the original file did not contain OXT, as you can see, it has O1 & O2, so I removed the O2 from the PDB and renamed O1 to OXT.

OK, so now that OXT is causing a problem, go back to the original version and don't introduce OXT. 

It does look like you're going to have a serious problem merging these chains... the termini are nowhere near each other!

If I recall your original problem correctly, you're trying to use pdb2gmx to generate a [moleculetype] that has multiple molecules in it so that you can use "inter-molecular" distance restraints in a GROMACS-legal intra-moleculetype way. If pdb2gmx is sensitive to chain ID, and the -chainsep/TER combination is suitable, then it's conceivable this would work in the way you hope, however it is not clear to me that pdb2gmx will have this functionality. -chainsep comments in pdb2gmx -h imply that a new chain and a new moleculetype go together.

There's no ready way to merge [moleculetype] .itp files after the fact. All the atom numbers after the first molecule would have to be renumbered, and their interactions likewise. That would be a job for Perl - read the first .itp file, count the atoms and break the file into chunks for each directive, then read each subsequent .itp file, break the file into chunks, add the appropriate integer to each atom number, and append the chunks. Finally, write out all the chunks. Regular expressions will probably be good friends there.

I seem to recall intent at some point to implement inter-molecular distance restraints in GROMACS to avoid this issue. I don't know if this was ever done, though. Check the manual and search the mailing list and wiki.

Mark
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