Hi Jack,
Look, if I understand well, what you want is to be able to something like
tleap does for amber, where you load all the libs you need, including the
ones you created for your ligand(s), and then generate the MD input files at
once needing just the complexed pdb or mol2 as input.
For
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CC: gmx-users@gromacs.org; a...@drugdiscoveryathome.com
Subject: [gmx-users] Re: including a custom itp file in topology
Hi Jack,
Look, if I understand well, what you want is to be able to something like tleap
does for amber, where you load all the libs you need, including the ones you
Hi Berk,
If pdb2gmx will do what you said below, then for me the feature is
delivered.
To be sure, what I would like to have (and I guess Jack too) is:
- one has a pdb with protetin + ligands (one or more)
- have the topologies itp files for the ligands already created
- run pdb2gmx on
Dear Berk,
I beg your pardon, but I have to assume that what you wrote below is not
correct so, right?
Should it be 'ligand.rtp' instead of 'ligand.itp'?
Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to
generate rtp files as well (but hdb and else probably not).
I confess I don't know the difference between rtp and itp. What I was hoping
was an easier way to generate topologies for complexes that have
non-standard residue names like LIG. Alan's acpypi works. You just have to
do some extra scripting. But it seems like pdb2gmx should have a way to load
the
Hi,
rtp stands for 'Residue ToPology' and is used exclusively for building
block definitions, which are only used by pdb2gmx.
itp stands for 'Include ToPology' and can contain any part of a
topological description of a system, atom types, bond types,
moleculetypes, definitions, to be #included at
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