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

From: Lachele Foley <>
Date: Thu, 26 Jun 2014 14:13:14 -0400

You almost have it! :-)

First things, tho: you can download updated parameters and use them,
even in an older leap. I recommend doing this. You just need to put
the files in the relevant places in the AMBERHOME tree or modify your
tleap and the file contents to point to the new location.

Current params:
All params, and docs for them:

The issue is that you combined the lig and receptor into the complex
before you issued the bond commands. When you combine, you make a new
thing that is the combination of the two others. So, when you modified
the bonds in "receptor", you were only modifying that and not the copy
of "receptor" that had now become part of "complex."

Try this variant, and do consider using the updated params instead of
06h. Also, the different file suffixes are nicer if using VMD to
check things.

source leaprc.GLYCAM_06h # or, better: leaprc.GLYCAM_06j-1
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG

receptor = loadPDB rec.pdb
bond receptor.901.C1 receptor.902.O4
bond receptor.902.C1 receptor.903.O4
bond receptor.903.C1 receptor.904.O4
bond receptor.904.C1 receptor.905.O4
bond receptor.905.C1 receptor.906.O4
bond receptor.906.C1 receptor.907.O4
bond receptor.907.C1 receptor.908.O4
bond receptor.908.C1 receptor.901.O4
check receptor

complex = combine {receptor LIG}

set default PBRadii mbondi2
saveAmberParm LIG LIG.parm7 LIG.rst7
saveAmberParm receptor rec.parm7 rec.rst7
saveAmberParm complex com.parm7 com.rst7
savepdb complex complex_gas.pdb
charge complex
addIons complex Na+ 0
solvateBox complex TIP3PBOX 8.0
saveAmberParm complex com_solvated.parm7 com_solvated.rst7
savepdb complex com_solvated.pdb

On Thu, Jun 26, 2014 at 8:46 AM, Shreeramesh <> wrote:
> 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
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Thu Jun 26 2014 - 11:30:02 PDT
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