Dear Paul, my molecule can't be too big for libcheck as I used libcheck successfully for molecules of exactly the same size before. Now, only one atom is different, but this atom is a heavy metal and therefore Acedrg won't work (also any program I tried to use with SMILES code just gives nonsense pdb and cif output because the molecule is quite complex). I also can't simply rewrite the atom name in the pdb and cif files I have for the old molecules, because the heavy metal changes the geometry. Maybe I could try to rewrite the files but it would mean manually editing a lot of bond lengths and angles which I know can be prevented by generating lib file from libcheck because I already did it previously for other similar molecules. So there must be something wrong either with my pdb I use as input in libcheck (but I couldn't figure out what) or the way I run libcheck.
Andrea On Thursday, August 15, 2024 17:13 CEST, Paul Emsley <[email protected]> wrote: On 8/15/24 09:01, Andrea Smith wrote: > > -- > > Dear all, > Dear Andrea, > > I successfully used libcheck to generate libraries for my ligands a > couple of months ago. Now I wanted to use it again and it is giving me > an error. Moreover, even though I select COOR Y and LCOOR N, libcheck > uses COOR N and LCOOR Y. > That is chemistry-perception mode, it seems to me (it's been a while since I've used it). > > Can someone tell me what am I doing wrong? > You are doing nothing wrong. You have a big molecule. > > I attach a prinscreen from my terminal window. I am using Linux > Ubuntu, Libcheck vers 5.2.02 (which I used successfully previously). > Fascinating. Libcheck is telling you to edit the Fortran code and recompile it. But who's up for that? The alternative is to use Acedrg. However, the current version of Acedrg doesn't do chemistry perception - so you will have to draw the molecule out in 2D (or by some other means determine the SMILES string). Paul. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
