On 11/9/19 9:30 PM, Daniel Burns wrote:
Thank you!
Should my ligands have identical names in the .gro file?
For a normal MD simulation, there's no reason to treat the ligands
differently in any way. You have two copies of the same molecule, so you
only need one ligand topology and you need to note that there are two of
these same molecules in the [molecules] directive.
-Justin
On Fri, Nov 8, 2019 at 6:23 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 11/8/19 4:25 PM, Daniel Burns wrote:
Hello,
I am trying to simulate a dimer with identical ligands bound on each
subunit.
I generated the ligand files with cgenff.
I have Liga and Ligb files that each have identical contents (the
filenames, residue, and molecule name are different though). I am only
getting errors on the Ligb.prm file in the [dihedral types] section. The
problematic section repeats the i, j, k, and l atoms for 3 or more lines
but each line has different phi and kphi values. The error is shown
below
along with the section of the ligb.prm file that presents the issue.
Thank you for your time!
Dan
ERROR 9 [file ligb.prm, line 42]:
Encountered a second block of parameters for dihedral type 9 for the
same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
The troublesome lines from ligb.prm:
CG2R61 CG2R61 CG321 NG2R51 9 0.000000 0.497896 2
CG2R61 CG2R61 CG321 NG2R51 9 180.000000 0.552288
4
CG2R61 CG2R61 CG321 NG2R51 9 180.000000 0.054392
6
CG2R61 CG321 NG2R51 CG2R51 9 0.000000 1.610840
1
CG2R61 CG321 NG2R51 CG2R51 9 0.000000 1.757280
2
CG2R61 CG321 NG2R51 CG2R51 9 0.000000 0.334720
3
CG2R61 CG321 NG2R51 CG2R51 9 0.000000 0.230120
4
CG2R61 CG321 NG2R51 NG2R50 9 180.000000 1.610840
1
CG2R61 CG321 NG2R51 NG2R50 9 0.000000 1.757280
2
CG2R61 CG321 NG2R51 NG2R50 9 180.000000 0.334720
3
CG2R61 CG321 NG2R51 NG2R50 9 0.000000 0.230120
4
If the ligands are topologically identical, their bonded parameters can
only appear once in the topology. You can't simply #include both
topologies (despite giving them different [moleculetype] names) because
their bonded parameters will be repeated, therefore triggering this error.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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