From: yjcoshc (yjcoshc_at_gmail.com)
Date: Wed Jul 22 2020 - 16:51:03 CDT
Hi Selemon,
Would you mind sending an example input for debugging?
Thanks,
Haochuan Chen
在 2020/7/22 下午4:33, Selemon Bekele 写道:
>
> 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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