Re: [AMBER] dlpc membrane

From: <jojartb.jgypk.u-szeged.hu>
Date: Tue, 15 Nov 2016 06:17:49 +0100

Dear David,
Thank you very much for this solution!
I tried your suggestion. If only leaprc.water.tip3p and leaprc.lipid14
files are included, than tleap did not recognize water.
Error:
For atom: .R<WAT 4>.A<O 1> Could not find vdW (or other) parameters
for type: OW
For atom: .R<WAT 4>.A<H1 2> Could not find vdW (or other) parameters
for type: HW
For atom: .R<WAT 4>.A<H2 3> Could not find vdW (or other) parameters
for type: HW
Therefore i incuded the leaprc.protein.ff14SB file and everything
working fine.
Thank you for your help again!
Best regards, Balazs


Id├ęzet (David A Case <david.case.rutgers.edu>):

> On Mon, Nov 14, 2016, jojartb.jgypk.u-szeged.hu wrote:
>
>> here I send you the pdb file and the tleap file.
>
> OK: here's the problem: the leaprc.water.tip3p file has a residue
> called "LA",
> which overwrites the lipid14 residue of the same name. [In my partial
> defense, if you had followed the suggestions in my earlier email, this would
> have become obvious.]
>
> This is a general problem we have: Amber developers often feel free to invent
> their own residue names, that may conflict with those defined by the PDB.
> In this case, "LA" is a PDB-reserved name for the La(III) ion, and is
> correctly used in leaprc.water.tip3p. The leaprc.lipid14 file is trying to
> re-use this name for something entirely different.
>
> A workaround for this case should be (untested!) to load leaprc.water.tip3p
> first, then leaprc.lipid14 second.
>
> Thanks for the report--we'll have to try to figure out a better long-term
> solution.
>
> ....dac
>
>
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Received on Mon Nov 14 2016 - 21:30:02 PST
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