Re: vmd-l: Multiple residues at same position

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Apr 16 2006 - 08:38:30 CDT

This sort of thing can show up in a PDB file for a variety of reasons;
it's possible that the isoleucine is assigned an odd numbering to keep
the rest of the numbering consistent with some well-known alignment, or
that there was a mutant used in the same study, or something along those
lines. You should check the crystallography paper to see what is going
on with this residue, and either delete one of the alternatives or let
NAMD renumber it, depending on the reason for the numbering being this way.
Peter

snoze pa wrote:

> 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
>

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