VMD-L Mailing List

From: Nadira Khatoon (Nadira.Khatoon_at_bioschool.iitd.ac.in)
Date: Fri Apr 04 2025 - 03:58:16 CDT

Hello all,

I am trying to get binding energy using cafe plugin of VMD. But the PB
solver is giving me the parsing error. The execution command is: mmpbsa
-top 9awj_2nic_final.psf -trj eq2_WT.dcd -first 100 -last 100 -out
mmpbsa_100 -com "all" -rec "protein" -lig "resname LIG" -pb 1 -pb_exe
"/usr/bin/apbs" -sa 1 -sa_exe "/usr/bin/apbs" -par par_all36_lipid.prm
-par par_all36_cgenff.prm -par par_all36m_prot.prm -par lig.prm -par
toppar_water_ions.str
Can someone help me solve this issue? The mm (not included in the above)
and sa part is working fine.

CaFE) Sanity check
CaFE) Found 325914 atoms for complex
CaFE) Found 32944 atoms for receptor
CaFE) Found 54 atoms for ligand
CaFE) Loaded 414 frames for complex
CaFE) Generating new trajectory for complex
CaFE) Loaded 1 frames for complex
CaFE) It took 0 days 0 hrs 0 min 2 sec
CaFE) Calculating the PB term
NOsh_parseInput: Ignoring undefined keyword in(modpdb4!
NOsh_parseInput: Ignoring undefined keyword file!
NOsh_parseInput: Ignoring undefined keyword "com_pb_tmp_100.pqr"!
NOsh_parseInput: Ignoring undefined keyword format!
NOsh_parseInput: Ignoring undefined keyword pqr)!
NOsh_parseInput: Ignoring undefined keyword acenter(-0.7787190079689026!
NOsh_parseInput: Ignoring undefined keyword -0.9324414134025574!
NOsh_parseInput: Ignoring undefined keyword 10.994101524353027)!
NOsh_parseInput: Ignoring undefined keyword indi!
NOsh_parseInput: Ignoring undefined keyword 1.0!
NOsh_parseInput: Ignoring undefined keyword exdi!
NOsh_parseInput: Ignoring undefined keyword 80.0!
NOsh_parseInput: Ignoring undefined keyword scale!
NOsh_parseInput: Ignoring undefined keyword 2.0!
NOsh_parseInput: Ignoring undefined keyword perfil!
NOsh_parseInput: Ignoring undefined keyword 80.0!
NOsh_parseInput: Ignoring undefined keyword prbrad!
NOsh_parseInput: Ignoring undefined keyword 1.4!
NOsh_parseInput: Ignoring undefined keyword linit!
NOsh_parseInput: Ignoring undefined keyword 1000!
NOsh_parseInput: Ignoring undefined keyword maxc!
NOsh_parseInput: Ignoring undefined keyword 0.0001!
NOsh_parseInput: Ignoring undefined keyword bndcon!
NOsh_parseInput: Ignoring undefined keyword 4!
NOsh_parseInput: Ignoring undefined keyword energy(s!
NOsh_parseInput: Ignoring undefined keyword g)!
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
You didn't specify any molecules (correctly)!
Bailing out!
Error reading molecules! 

-- 
Nadira