Dear all, Good day
I am sorry if the question has been asked before. I was doing tutorial B5
for the green fluorescent protein.
I prepared the gfp.pdb file using the pdb4amber tool. made the
modifications suggested to the Methionine amino acids. Then when I ran the
tleap in Step 4, an error was reported
Created a new atom named: H3 within residue: .R<VAL 65>
and then the programme quit with the message
FATAL: Atom .R<VAL 65>.A<H3 17> does not have a type.
when I opened the file I noticed, there was another difference from the
uploaded sample file.
my prepared file after following the commands
ATOM 1 N SER A 1 28.888 9.409 52.301 1.00 85.05
N
ATOM 2 CA SER A 1 27.638 10.125 52.516 1.00 80.05
C
ATOM 3 C SER A 1 26.499 9.639 51.644 1.00 85.36
C
ATOM 4 O SER A 1 26.606 8.656 50.915 1.00 84.56
O
ATOM 5 CB SER A 1 27.783 11.635 52.378 1.00 70.97
C
ATOM 6 OG SER A 1 27.690 12.033 51.012 1.00 44.08
O
*ATOM 7 H1 SER A 1 29.229 9.026 53.206 1.00 85.05
H ATOM 8 H2 SER A 1 28.730 8.628 51.632 1.00 85.05
H ATOM 9 H3 SER A 1 29.599 10.061 51.911 1.00 85.05
H *
ATOM 10 HA SER A 1 27.382 9.898 53.551 1.00 80.05
H
ATOM 11 HB2 SER A 1 27.007 12.133 52.960 1.00 70.97
H
ATOM 12 HB3 SER A 1 28.742 11.951 52.788 1.00 70.97
H
ATOM 13 HG SER A 1 27.784 13.006 50.948 1.00 44.08
H
..........................................................
the provided sample has no such atoms
ATOM 1 N SER A 1 28.888 9.409 52.301 1.00 85.05
N
ATOM 2 CA SER A 1 27.638 10.125 52.516 1.00 80.05
C
ATOM 3 C SER A 1 26.499 9.639 51.644 1.00 85.36
C
ATOM 4 O SER A 1 26.606 8.656 50.915 1.00 84.56
O
ATOM 5 CB SER A 1 27.783 11.635 52.378 1.00 70.97
C
ATOM 6 OG SER A 1 27.690 12.033 51.012 1.00 44.08
O
ATOM 7 HA SER A 1 27.382 9.898 53.551 1.00 80.05
H
ATOM 8 HB2 SER A 1 27.007 12.133 52.960 1.00 70.97
H
ATOM 9 HB3 SER A 1 28.742 11.951 52.788 1.00 70.97
H
ATOM 10 HG SER A 1 27.784 13.006 50.948 1.00 44.08
H
............................................................................
Not sure how it happened. Has this happened previously?
When I use the example file for tleap, no error is generated and the
parameter files can be generated.
Also if lets say I manually edit this file , what is the command for
renumbering the residues
Really appreciate your help.
Thank you
Regards
Ayesha
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Received on Sun Aug 23 2020 - 11:30:02 PDT
