AMBER Archive (2003)

Subject: Re: Problem with a library

From: David A. Case (case_at_scripps.edu)
Date: Fri Jun 13 2003 - 16:07:37 CDT

On Fri, Jun 13, 2003, Frederico.Miranda_at_ibmb.uib.no wrote:

> Hye, I made a library for a phosphoserine based on the library for the serine
> residue and the phosphate groups of nucleic acids residues (charges were
> calculated for a phosphoserine). Here is my input file:
>
> ________________________________________________________________________________
>
> 0 0 2
>
> PHOSPHOSERINE
> sep.db4
> SEP INT 1
> CORR OMIT DU BEG
> 0.00000
> 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
> 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
> 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
> 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
> 5 H H E 4 3 2 1.010 119.800 0.000 0.27190
> 6 CA CT M 4 3 2 1.449 121.900 180.000 0.028
> 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08430
> 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.105
> 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.066
> 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.066
> 11 OG OS M 8 6 4 1.430 109.470 180.000 -0.491
> 12 P P M 11 8 6 1.600 119.040 200.000 1.493

I think you want atoms 11 and 12 to be "S" (side chain), not "M" (main chain)

> 13 O1P O2 E 12 11 8 1.480 109.610 180.000 -0.913
> 14 O2P O2 E 12 11 8 1.480 109.580 60.000 -0.913
> 15 O3P O2 E 12 11 8 1.480 109.590 300.000 -0.913
> 16 C C M 6 4 3 1.522 111.100 180.000 0.59730
> 17 O O E 16 6 4 1.229 120.500 0.000 -0.56790
>

> WARNING: There is a bond of 4.799280 angstroms between:
> ------- .R<SEP 16>.A<P 9> and .R<SEP 16>.A<C 13>

As LEaP is saying, since both the phosphorus and the carbonyl carbon are
main chains, they are bonded together.

You can always use the "desc" command in LEaP to find out what the bonding
pattern is; or (easier) just "edit" your residue in xleap, and look at it.

> WARNING: There is a bond of 9.923259 angstroms between:
> ------- .R<LEU 136>.A<C 18> and .R<ASP 137>.A<N 1>

The above seems to be a separate (but still serious problem): there is a gap
of 10 Ang. between residues 136 and 137; you need to check your pdb file.

> ERROR: The unperturbed charge of the unit: -10.502100 is not integral.
> WARNING: The unperturbed charge of the unit: -10.502100 is not zero.

The charges in your residue above sum to -1.5021, rather than -2. You will
need to fix this. (I am assuming you really want the double-deprotonated
phosphate, i.e. you are at alkaline pH).

..good luck...dac 

-- 

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