From: Selemon Bekele (selemon_at_uakron.edu)
Date: Wed Jul 22 2020 - 16:33:33 CDT
Dear NAMD developers and users,
I recently downloaded the NAMD package and installed it
with mpi. When I try to run, I got the error message
FATAL ERROR: must have same number of LP hosts as lone pairs
I tried to look it up in the NAMD mailing list in case somebody
had already encountered a similar issue but did not find a
solution. So, I searched in the source code where the error
message is printed and found out that it is in:
NAMD_2.14b2_Source/Linux-x86_64-g++/src/Molecule.C
===============
Lines 9454-9457
===============
if (is_lonepairs_psf && numLonepairs != numLphosts) {
NAMD_die("must have same number of LP hosts as lone pairs");
}
A print out of "numZeroMassAtoms" after the loop containing the
lines below shows that the number of zero mass atoms is correctly
calculated:
===============
Lines 1383-1387
===============
/* Parse up the line */
read_count=sscanf(buffer, "%d %s %s %s %s %s %f %f",
&atom_number, segment_name, residue_number,
residue_name, atom_name, atom_type, &charge, &mass);
if (mass <= 0.05) ++numZeroMassAtoms;
===============
However, the number of zero mass atoms is zero when assigned to
the number of lone pairs as shown below. If the number is hardwired
as in the commented line, everything works fine.
===============
Lines 9446-9447
===============
if (simParams->watmodel == WAT_TIP4 || is_lonepairs_psf) {
//numZeroMassAtoms = 53819; // These MUST be lonepairs.
numLonepairs = numZeroMassAtoms; // These MUST be lonepairs.
*****************************************
Unless there is something wrong I am doing, one does not want to
edit and compile for every new system. I appreciate if someone
can help resolve this issue. I have attached the log file for reference.
Thanks in advance,
Selemon
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