Thank you so much.
I compare phosphoaspartate library which I have created and psophoserine library
from Amber
parameter database, in my library there is connectivity prodblem.
PHOSPHOSERINE library:-
!entry.T1P.unit.childsequence single int
2
!entry.T1P.unit.connect array int
1
17
!entry.T1P.unit.connectivity table int atom1x int atom2x int flags
1 2 17
1 3 17
3 4 17
3 17 17
3 5 17
5 6 17
5 11 17
5 7 17
7 8 17
7 9 17
7 10 17
11 12 17
12 15 17
12 14 17
12 13 17
13 16 17
17 18 17
and in PHOSPHOASPARTATE which I have created :-
!entry.PHD.unit.childsequence single int
2
!entry.PHD.unit.connect array int
0
0
!entry.PHD.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 16 1
1 17 1
2 3 1
2 5 1
2 15 1
3 4 1
5 6 1
5 13 1
5 14 1
6 7 1
6 8 1
7 9 1
9 10 1
9 11 1
9 12 1
Here what are these number 1, 17 in phosserine library i.e.
entry.T1P.unit.connect array int
1
17
How I can modify phosphoaspartate library?
When I look sus.lib generated in tutorial
http://ambermd.org/tutorials/basic/tutorial4b/
connectivity in this library is also silmilar to pshosphoaspartate.
> On Sat, Jan 08, 2011, Sangita Kachhap wrote:
>>
>> I edited the PDB file remove TER card. When load it to tleap
>> with frcmod file and lib file tleap again adding TER card to thses position
>
> Something bad is happening....maybe your library doesn't have "head" and
> "tail" atoms identified. If they are missing, you need to add them -- compare
> your modified library to the original ASP one. Or, look at the phosphoserine,
> etc. residues in the contributed parameters database to see how they look
> different from yours.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 08 2011 - 09:00:02 PST
