VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Sun Apr 16 2006 - 02:01:35 CDT

Hi all,
I am simulating a small protein using NAMD. But in my protein two residues
are assigned to same position, 19.
How can I solve this problem before starting NAMD. Shall I use the first
residue or second residue? or it is okey
to start with both residues. When I am using psfgen using both residues then
psfgen remove A from second
residue and assign it a next number, which in current case is 20(19 replaced
by 20 for ILE). I don't know how to
deal with this situation.
thanks in advance
snoze
Here is the input file.
ATOM 716 N GLU G 19 -5.502 -5.494 35.616 1.00149.39
N
ATOM 717 CA GLU G 19 -5.247 -4.252 34.895 1.00148.29
C
ATOM 718 C GLU G 19 -4.003 -4.347 34.019 1.00147.73
C
ATOM 719 O GLU G 19 -4.088 -4.687 32.838 1.00146.53
O
ATOM 720 CB GLU G 19 -5.080 -3.100 35.888 1.00148.27
C
ATOM 721 CG GLU G 19 -6.149 -3.054 36.967 1.00148.79
C
ATOM 722 CD GLU G 19 -5.945 -1.909 37.939 1.00148.76
C
ATOM 723 OE1 GLU G 19 -4.833 -1.792 38.496 1.00148.26
O
ATOM 724 OE2 GLU G 19 -6.899 -1.131 38.149 1.00148.68
O
ATOM 725 N ILE G 19A -2.851 -4.045 34.614 1.00147.61
N
ATOM 726 CA ILE G 19A -1.565 -4.072 33.921 1.00147.08
C
ATOM 727 C ILE G 19A -1.684 -3.661 32.455 1.00146.30
C
ATOM 728 O ILE G 19A -1.674 -4.505 31.559 1.00145.89
O
ATOM 729 CB ILE G 19A -0.897 -5.474 34.014 1.00147.76
C
ATOM 730 CG1 ILE G 19A -1.845 -6.558 33.491 1.00148.35
C
ATOM 731 CG2 ILE G 19A -0.503 -5.762 35.457 1.00147.20
C
ATOM 732 CD1 ILE G 19A -1.244 -7.951 33.480 1.00146.09
C