Dear
Dr. Lachele
,
I am Ramesh
and
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
"END".
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.
........
Ramesh
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- application/octet-stream attachment: tleap.all
Received on Thu Jun 26 2014 - 06:00:02 PDT
