I am currently having a similar problem. But instead of the blank lines, my
MOL2 file has .<TRIPOS>UNITY_ATOM_ATTR section between the ATOM and BOND
sections. This causes antechamber to make the coordinates of the last atom
repeated multiple times. I did the following changes on mol2.c and it works
for me (but should not work for the blank line problem).
-----
.. -53,6 +53,9 ..
}
if (strcmp(".<TRIPOS>BOND", tmpchar1) == 0) {
bondrecord = 1;
+ continue;
+ }
+ if (atomrecord == 1 && strncmp(".<TRIPOS>", tmpchar1, 9) == 0) {
/* end of atoms */
atomrecord = 0;
continue;
}
All the best,
Junjun
-----
On Fri, Jan 8, 2021 at 11:01 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Jan 06, 2021, Mateusz Bieniek wrote:
> >
> >I could use a bit of help with a strange situation with the .mol2 format.
> >There is an empty line in my .mol2 file just before the ".<TRIPOS>BOND"
> >section. This is a file generated by another package.
> >
> >It seems to me that the mol2 format defined Blank Line which is ignored by
> >the MOL2 command (http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf,
> >page 3).
> >
> >However, to my surprise, when I use antechamber
> >antechamber -i test.mol2 -fi mol2 -o out.mol2 -fo mol2 -dr no
> >
> >It generates an extra atom in my file in the ATOM section.
>
> Thanks for your report. I'm cc-ing to Scott and Junmei, who are probably
> in
> the best position to make sure that antechamber is ignoring blank lines in
> mol2 files.
>
> ....dac
>
>
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Received on Thu Feb 04 2021 - 12:30:02 PST
