Re: [AMBER] dlpc membrane

From: <jojartb.jgypk.u-szeged.hu>
Date: Mon, 14 Nov 2016 14:38:28 +0100

Dear David,
Thank you for your help.
In my first email i wrote, that I did not find any inconsistency
between the naming scheme in the pdb file and in lipid14.lib file.
In the leap.log one can see that the LA residue is loaded
>> loadoff lipid14.lib
Loading library: /opt/amber16/dat/leap/lib/lipid14.lib
Loading: CHL
Loading: LA
Loading: MY
Loading: OL
Loading: PA
Loading: PC
Loading: PE

Splitting the mol into PC and LA is also successfull:

Warning: name change in pdb file residue 1 ;
  this residue is split into LA and PC.
.
.

All this messages I have seen on other leap.log files regarding
different membrane lipids and there was everything fine.
Best, Balazs



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

> On Mon, Nov 14, 2016, jojartb.jgypk.u-szeged.hu wrote:
>
>> Created a new atom named: C12 within residue: .R<LA 1>
>> Created a new atom named: H2R within residue: .R<LA 1>
>
> This means that the pdb file you are loading has an atom named "C12" in
> residue 1. But the library file for residue "LA" does not have such an atom
> name.
>
> Try this: after you load the libraries, type "list" at the tleap prompt, to
> see the list of residues that tleap knows about. Then type "desc
> LA.1" to see
> the list of atom names inside the LA residue. That should help in debugging.
> Of course, if "LA" is not in the list of known residues, you would have to
> work on finding out why.
>
> ...dac
>
>
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Received on Mon Nov 14 2016 - 06:00:03 PST
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