After doing some digging I found that cpptraj can do the stripping
(Should have read the manual more thoroughly...).
The main reason for my question is... When I used a PDB as a prmtop in
ptraj, the "analyze matrix" routine failed (eigenvalue 0 0.00), possibly
because the pdb doesn't include the information included in the prmtop.
When I used this stripped prmtop in ptraj and plugged that in,
everything was OK.
Either case, thank you for the input.
Cihan
Cihan Aydin
University of Massachusetts Medical School
Department of Biochemistry and Molecular Pharmacology
PhD Candidate, Schiffer Lab
364 Plantation St LRB 970M
Worcester, MA 01605
cihan.aydin.umassmed.edu
On 2/7/2012 8:03 PM, David A. Case wrote:
> On Tue, Feb 07, 2012, Cihan Aydin wrote:
>> 1- Strip hydrogens or any other atoms that I want from the prmtop (not
>> only waters)?
>> 2- Create topologies using any version of leap without adding hydrogens
>> or other atoms?
> Essentially "no" to both questions. Why do you want to do something like
> this? That is, what would you do with such a stripped prmtop file if you
> made it? (A prmtop file without hydrogens wouldn't be of much (any?) use
> inside the Amber suite of programs.)
>
> ....dac
>
> [About the "essentially" part: one could imagine having "united atom"
> libraries that don't have hydrogens, e.g. ff03ua. Then hydrogens would not
> be added, because they are not needed for that force field. But that just
> applies to hydrogens bonded to carbon: hydrogens bonded to N or O would still
> be needed.]
>
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Received on Tue Feb 07 2012 - 18:00:02 PST
