VMD-L Mailing List

From: vivek sharma (vivek.sharma_at_helsinki.fi)
Date: Wed Dec 01 2004 - 11:58:46 CST

Dear Sir,

I am using solvate program via VMD with available psf and pdb files
(generated by psfgen). When I run Solvate from tkcon using commands in
console,

package require solvate
solvate xyz.psf xyz.pdb -t 5 -o abc_wat

everything goes fine, solvate runs, but warnings are shown in console as
shown below for each and every atom of pdb used;

------------------------------------
Warning: failed to set coordinate for atom H1 TIP3:15 WATE
no segment WATE
Warning: failed to set coordinate for atom H2 TIP3:15 WATE
no segment WATE
Warning: failed to set coordinate for atom OH2 TIP3:17 WATE
no segment WATE
Warning: failed to set coordinate for atom H1 TIP3:17 WATE
no segment WATE
-------------------------------------
and finally generated abc_wat.pdb file contains solvation water properly
but all original protein coordinates are not shown, something of this type
is shown,

------------------------

ATOM 1 N PHE 2 0.000 0.000 0.000 -1.00 0.00
CHAINA
ATOM 2 HT1 PHE 2 0.000 0.000 0.000 -1.00 0.00
CHAINA
ATOM 3 HT2 PHE 2 0.000 0.000 0.000 -1.00 0.00
CHAINA
ATOM 4 HT3 PHE 2 0.000 0.000 0.000 -1.00 0.00
CHAINA
ATOM 5 CA PHE 2 0.000 0.000 0.000 -1.00 0.00
CHAINA
ATOM 6 HA PHE 2 0.000 0.000 0.000 -1.00 0.00
CHAINA

-------------------------

I have checked that solvation water present after the protein atoms in
this same pdb has coordinates but these original atoms does not.
What can be the reason? Please explain.

sincerely,

Vivek Sharma 

-- 
VIVEK SHARMA
HBG BI