VMD-L Mailing List

From: denilson_at_dqi.ufla.br
Date: Mon Oct 03 2011 - 11:18:01 CDT

Dear all,

Please, substitute "NAMD (using the same topology and stream file" for "NAMD (using the same stream file and the parameter file par_all27_prot_lipid.prm" in the message a sent a couple of hours ago (see copy below).

Best regards.

Denilson.

Dear all

I am using VMD 1.9 on a Windows 7 (64 bits) machine to prepare the psf and pdb files for a molecular dynamics simulation using NAMD 2.8 on a Sun Fire X2200 station. Initially, a pdb file containing a protein, water and retinol, is converted to the corresponding pdb and psf files using AUTOPSF with the topology file top_all27_prot_lipid.rtf and the stream file toppar_all_22_prot_retinol.str (necessary to deal with retinol). The resulting psf and pdb files seemed to be OK. Then I used SOLVATE (solvate file.psf file.pdb -t value -o outputfile) to put everything inside a water box. In this step I observed that SOLVATE removed informations about the angles of the water molecules coming from the initial pdb file. The resulting system was neutralized witih AUTOIONIZE (8 Na+ were added) and submitted to NAMD (using the same topology and stream file, and rigid water settle algorithim), which did not carry out the calculations because:

"Info: 0 NBTHOLE_PAIRS

Warning: Ignored 956 bonds with zero force constants.

Warning: Will get H-H distance in rigid H2O from H-O-H angle.

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (ATOMS 2211 2213 2212)

------------- Processor 0 Exiting: Called CmiAbort ------------

Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (ATOMS 2211 2213 2212)

Charm++ fatal error:

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (ATOMS 2211 2213 2212)"

Apparently, this problem was caused by SOLVATE that removed the angle information when the water box was built.

I would appreciate if somebody could help me.

Best regards.

Denilson.