On Fri, Mar 21, 2014 at 11:57 PM, Nelson Max <max.cs.ucdavis.edu> wrote:
> Dear Jason,
>
> Thanks for the quick reply. I do not know if I am supposed to reply to the
> AMBER mailing just or just to you, so I am doing both. I did not find any
> string with "error" in the tleap.out file. In a separate e-mail just to you
> I will attach the files
>
> .
>
Replying to the list is the correct thing to do.
The end of the tleap.out file has a lot of messages like this:
FATAL: Atom .R<ILE 127>.A<HN 20> does not have a type.
FATAL: Atom .R<ILE 127>.A<HG11 21> does not have a type.
FATAL: Atom .R<SER 128>.A<HN 12> does not have a type.
FATAL: Atom .R<SER 128>.A<HB1 13> does not have a type.
FATAL: Atom .R<CASN 129>.A<HN 16> does not have a type.
FATAL: Atom .R<CASN 129>.A<HB1 17> does not have a type.
It appears that all of the H atoms have 'wrong' names (that do not conform
to the PDB standard used in the Amber library files). You can use the
reduce program to get rid of hydrogen atoms and then use reduce again to
put the hydrogen atoms back (with the correct names).
reduce -Trim your.pdb > your_noH.pdb
reduce your_noH.pdb > your_newH.pdb
Then try using your_newH.pdb instead with the NAB program.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 21 2014 - 21:30:03 PDT
