VMD-L Mailing List

From: Rajat Chakraborty (rajat.buet_at_gmail.com)
Date: Mon Oct 10 2022 - 13:06:00 CDT

Hello,

I was trying to solvate my structure using the basic solvate command. I got
the following message:

psfgen) Warning: failed to set coordinate for atom SE MOS:1720 SHT
psfgen) Warning: failed to set coordinate for atom SE MOS:1723 SHT
psfgen) Warning: failed to set coordinate for atom SE MOS:1726 SHT

This was the case for all Se atoms. The solvated psf and pdb files were
created however. But the pdb file contained zeros as the coordinate.

I am providing part of the input and output files codes as samples. It
would be great if you can help. Thanks.

Best,
Rajat

input.psf:
    1720 SHT 1720 MOS Se SE2 0.000000 75.9190 0
    1721 SHT 1721 MOS S SM2 0.000000 32.0650 0
    1722 SHT 1722 MOS MO MO 0.000000 95.9400 0
    1723 SHT 1723 MOS Se SE2 0.000000 75.9190 0
    1724 SHT 1724 MOS S SM2 0.000000 32.0650 0
    1725 SHT 1725 MOS MO MO 0.000000 95.9400 0
    1726 SHT 1726 MOS Se SE2 0.000000 75.9190 0

input pdb:
ATOM 1720 Se MOS S1720 28.713 -9.123 1.565 1.00 0.00 SHT
SE
ATOM 1721 S MOS S1721 28.713 -9.123 -1.565 1.00 0.00 SHT
 S
ATOM 1722 MO MOS S1722 28.713 -7.281 -0.000 1.00 0.00 SHT
MO
ATOM 1723 Se MOS S1723 27.118 -6.361 1.565 1.00 0.00 SHT
SE
ATOM 1724 S MOS S1724 27.118 -6.361 -1.565 1.00 0.00 SHT
 S
ATOM 1725 MO MOS S1725 23.927 -4.519 -0.000 1.00 0.00 SHT
MO
ATOM 1726 Se MOS S1726 22.332 -3.598 1.565 1.00 0.00 SHT
SE

solvate.tcl:
set sys input
package require solvate
solvate ${sys}_final.psf ${sys}_final.pdb \
-minmax {{-45 -45 -45} {45 45 45}} -o solvate_sol

solvate_sol.psf:
    1720 SHT 1720 MOS Se SE2 0.000000 75.9190 0
    1721 SHT 1721 MOS S SM2 0.000000 32.0650 0
    1722 SHT 1722 MOS MO MO 0.000000 95.9400 0
    1723 SHT 1723 MOS Se SE2 0.000000 75.9190 0
    1724 SHT 1724 MOS S SM2 0.000000 32.0650 0
    1725 SHT 1725 MOS MO MO 0.000000 95.9400 0
    1726 SHT 1726 MOS Se SE2 0.000000 75.9190 0

solvate_sol.pdb:
ATOM 1720 Se MOS S1720 0.000 0.000 0.000 -1.00 0.00 SHT

ATOM 1721 S MOS S1721 28.713 -9.123 -1.565 1.00 0.00 SHT
 S
ATOM 1722 MO MOS S1722 28.713 -7.281 -0.000 1.00 0.00 SHT
MO
ATOM 1723 Se MOS S1723 0.000 0.000 0.000 -1.00 0.00 SHT

ATOM 1724 S MOS S1724 27.118 -6.361 -1.565 1.00 0.00 SHT
 S
ATOM 1725 MO MOS S1725 23.927 -4.519 -0.000 1.00 0.00 SHT
MO
ATOM 1726 Se MOS S1726 0.000 0.000 0.000 -1.00 0.00 SHT