AMBER Archive (2005)

Subject: Re: AMBER: ambpdb TER problems

From: Sam (samuel.arey_at_epfl.ch)
Date: Tue Dec 27 2005 - 10:23:39 CST


David A. Case wrote:

>Can you post the "protein.pdb" file? Do you have the same TER card problem
>if you don't solvate things? [That would allow us to create a much smaller
>test case....]
>
>...thanks...dac

Indeed, it turns out that the ambpdb-misplacement of TER card
only happens after I have solvated the structure. Curious.. This
is independent of whether or not I have added K+ ions to the
structure (or in which order I do these two steps).

An xleap "check" of the solvated structure does not reveal any
"close contact" warnings with respect to water molecules with
either the CSER or DA5 residues.

I have temporarily posted the following files for xleap manipulation
of protein.pdb. Please note that the residue modification libraries
are unpublished works-in-progress and are not yet intended to be
used as "optimized" parameterizations.

http://lcbcpc21.epfl.ch/Group_members/sam/omc.top

http://lcbcpc21.epfl.ch/Group_members/sam/leaprc

http://lcbcpc21.epfl.ch/Group_members/sam/protein.pdb

http://lcbcpc21.epfl.ch/Group_members/sam/frcmod.FS4

http://lcbcpc21.epfl.ch/Group_members/sam/frcmod.8OG

http://lcbcpc21.epfl.ch/Group_members/sam/anti-8OG.prep

http://lcbcpc21.epfl.ch/Group_members/sam/CYG.lib

http://lcbcpc21.epfl.ch/Group_members/sam/FS4ox.lib

Thanks for your help --
Sam

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