50
complex.pdb. In the “Save multiple models in” box choose “a
single file.”
2. In order to save the separate molecular structures select CC as
described before (CTRL+ click on one atom and press the up
arrow to expand selection) and then click Actions → Atoms/
Bonds → Delete. Save the 2-HP-B-CD structure as 2-HPBCD.pdb and one more time as 2-HP-B-CD.mol2.
3. Close the Chimera window and then reopen it. Press
File → Open and open the complex.pdb file that you previously
saved. In a similar manner, select and delete the 2-HP-B-CD
structure. Now save the CC structure both in .pdb and .mol2
format. For a more thorough procedure see Note 1.
Visit the SwissParam server [11] in order to create topologies for
CC and 2-HP-B-CD using the Merck molecular force field
(MMFF) [12] (see Note 2).
1. Click browse and upload each separate molecule’s structure in
.mol2 format. There is no need to create topology for the complex, just for the two separate molecules. Press submit Query.
After a short while (approximately 1 min) click on the link provided in the website in order to download the files that were
created by the server.
2. Extract the file from the downloaded zipped folder and copy
the gromacs topology file for each molecule (file extension .itp)
in your working directory.
3. In a text editor, open CC.itp (or however the SwissParam server
named your topology file for the CC molecule). Cut all lines
before [moleculetype]. Create a blank text document, name it
atomCC.itp, and paste all the information that you cut from the
topology file before. These specific steps were added in order to
avoid the frequent gromacs error “Invalid order for the directive [molecule type]”; see Note 3 for further information.
Repeat for the 2-HP-B-CD.itp file.
4. In this simulation, 2-HP-B-CD will be restrained and the relevant drug molecule CC will be pulled out of the CD’s cavity. In
order to keep the host molecule restrained, open the 2-HPBCD.itp file in a text editor and paste the following lines in the
bottom:
#ifdef POSRES_B
#include "posreCYCL.itp"
#endif
(If you are using the vi editor, in order to edit the file press the letter “i,” paste the lines and then press ESC. In order to save the
file and quit press “:wq” and press enter.
3.1.3 Create
the Topology Files for Both
Drug and Host
Sofia Kiriakidi and Thomas Mavromoustakos
complex.pdb. In the “Save multiple models in” box choose “a
single file.”
2. In order to save the separate molecular structures select CC as
described before (CTRL+ click on one atom and press the up
arrow to expand selection) and then click Actions → Atoms/
Bonds → Delete. Save the 2-HP-B-CD structure as 2-HPBCD.pdb and one more time as 2-HP-B-CD.mol2.
3. Close the Chimera window and then reopen it. Press
File → Open and open the complex.pdb file that you previously
saved. In a similar manner, select and delete the 2-HP-B-CD
structure. Now save the CC structure both in .pdb and .mol2
format. For a more thorough procedure see Note 1.
Visit the SwissParam server [11] in order to create topologies for
CC and 2-HP-B-CD using the Merck molecular force field
(MMFF) [12] (see Note 2).
1. Click browse and upload each separate molecule’s structure in
.mol2 format. There is no need to create topology for the complex, just for the two separate molecules. Press submit Query.
After a short while (approximately 1 min) click on the link provided in the website in order to download the files that were
created by the server.
2. Extract the file from the downloaded zipped folder and copy
the gromacs topology file for each molecule (file extension .itp)
in your working directory.
3. In a text editor, open CC.itp (or however the SwissParam server
named your topology file for the CC molecule). Cut all lines
before [moleculetype]. Create a blank text document, name it
atomCC.itp, and paste all the information that you cut from the
topology file before. These specific steps were added in order to
avoid the frequent gromacs error “Invalid order for the directive [molecule type]”; see Note 3 for further information.
Repeat for the 2-HP-B-CD.itp file.
4. In this simulation, 2-HP-B-CD will be restrained and the relevant drug molecule CC will be pulled out of the CD’s cavity. In
order to keep the host molecule restrained, open the 2-HPBCD.itp file in a text editor and paste the following lines in the
bottom:
#ifdef POSRES_B
#include "posreCYCL.itp"
#endif
(If you are using the vi editor, in order to edit the file press the letter “i,” paste the lines and then press ESC. In order to save the
file and quit press “:wq” and press enter.
3.1.3 Create
the Topology Files for Both
Drug and Host
Sofia Kiriakidi and Thomas Mavromoustakos