AMBER Archive (2008)

Subject: Re: AMBER: ptraj closest command

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Mon Nov 17 2008 - 10:51:42 CST

Hi Thomas,

This is a know bug in ptraj and, the last I heard, Tom Cheatham's was
going to look at it. The temporary solution is to use ptraj from
Amber9.

HTH,
Gustavo.

On Mon, Nov 17, 2008 at 11:14 AM, wrote:
> Hi Amber users,
>
> Im having trouble using ptraj's closest command to select a few water
> molecules closest to a solute. Heres my input:
>
> --------------------------------------------------------------
> trajin ph0_wat_pro.crd_img
> solvent byres :WAT
> closest 3 @1
> trajout ph0_wat_pro.crd_img_3w pdb
> --------------------------------------------------------------
>
> the coordinate file read is centered on molecule 1 and imaged.
> ptraj runs fine and gives output that looks unsuspicious:
>
> --------------------------------------------------------------
> PTRAJ: Processing input from "STDIN" ...
>
> PTRAJ: trajin ph0_wat_pro.crd_img
> Checking coordinates: ph0_wat_pro.crd_img
>
> PTRAJ: solvent byres :WAT
> Mask [:WAT] represents 2259 atoms
> Searching for solvent by mask :2-754
>
> PTRAJ: closest 3 @1
> Mask [@1] represents 1 atoms
>
> PTRAJ: trajout ph0_wat_pro.crd_img_3w pdb
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 1000 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (ph0_wat_pro.crd_img) is an AMBER trajectory (with box info) with
> 1000 sets
>
> OUTPUT COORDINATE FILE
> File (ph0_wat_pro.crd_img_3w) is a PDB file
>
> ACTIONS
> 1> CLOSESTWATERS: saving the 3 closest solvent molecules around atoms
> :1_at_P1
> The current solvent mask is :2-754
>
>
> Processing AMBER trajectory file ph0_wat_pro.crd_img
> ....
> -----------------------------------------------------------
>
> but the pdb files produced do not contain the closest waters:
>
> e.g.:
>
> REMARK 1 PDB file generated by ptraj (set 1000)
> ATOM 1 P1 po4 1 0.008 0.012 0.000 0.00 0.00
> [...]
> TER 0 0
> ATOM 12 O WAT 4 12.041 -7.377 -10.470 0.00 0.00
> ATOM 13 H1 WAT 4 12.964 -7.450 -10.712 0.00 0.00
> ATOM 14 H2 WAT 4 12.043 -6.842 -9.677 0.00 0.00
>
> Visual inspection shows that there are water molecules much closer to the
> solute than the ones ptraj actually picks (the solute is small and the
> closest waters are no more than 3-4A away).
>
> Is there anything obvious I overlooked? Any suggestions what Im doing
> wrong? (Using the noimage command doesnt change anything, neither does
> picking the full residue :1 as mask in closest)
>
> Kind Regards,
>
> Thomas
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