[AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg.

From: Shreeramesh <shreeramesh.gmail.com>
Date: Thu, 26 Jun 2014 05:46:31 -0700


Dr. Lachele

I am Ramesh

 Your suggestion was helpful to me to work in AMBER. However, still there
are some minor issues

to obtain a solvated complex​

You have given me the following suggestions:

1. Remove all lines from the PDB file that do not begin with "HETATM" or

I successfully removed
It removes the link between residue-1 and residue-8 only and keeps the link
between other residues

2. Change all the residue names from GLC to 4GA.

I successfully changed

3. Change these atom names: H62 and H63 to H61 and H62; HO2, HO3 and
HO6 to H2O, H3O and H6O.

​I successfully changed it

4. Add TER cards between each of the residues.

I successfully incorporated

5. Use the following, or something equivalent, as input to tleap.
This assumes you call your new pdb file "rec_modified.pdb".

source leaprc.GLYCAM_06j-1

m = loadpdb rec_modified.pdb

bond m.901.C1 m.902.O4
bond m.902.C1 m.903.O4
bond m.903.C1 m.904.O4
bond m.904.C1 m.905.O4
bond m.905.C1 m.906.O4
bond m.906.C1 m.907.O4
bond m.907.C1 m.908.O4
bond m.908.C1 m.901.O4

check m

saveamberparm m m.parm7 m.rst7

I also incorporated the above mentioned information in my tleap script
(tleap.all) except GLYCAM_06j-1 since it was not loaded in our AMBER 12.
Instead of GLYCAM_06j-1, I used GLYCAM_06h. The file (tleap.all) has been
enclosed in attachment.

*However, the glucose units are not linked in solvated complex and they are
appearing as the independent residues in the output of solvated complex. ​*

*If I remove the TER card between each of the residues in .pdb file of
gammacyclodextrin, all the residues are linked except residue-1 and
residue-8. *I also attached the .pdb file of gammacyclodextrin, tleap and
.pdb of solvated complex for your kind attention

I request you to kindly provide the solution to link all the residues of
gammacyclodextrin in solvated complex and I will be thankful to you for
your help.


AMBER mailing list

Received on Thu Jun 26 2014 - 06:00:02 PDT
Custom Search