Re: [AMBER] Load protein complex to Xleap (Combine)

From: Rilei Yu <>
Date: Sun, 29 Mar 2009 05:00:00 +0100

Dear Dr. David,
I am really very sorry for not explaining my problem distinctly!
When I obtained the protein complex which was produced by docking a small peptide into a receptor, I wanted to perform the MD on this complex. But when I load the complex into the xleap, I found there are some errors on the ligand. So I could not obtain the prepin and inpcrd of the protein complex (Protein-small peptide obtained by Flexx docking in sybyl).
In oder to better elaborate my problem, I want to put all my operation process in the following:
a = loadpdb procomplex.pdb
edit a
# I found some errors on this small peptide.
 saveamberparm a procomplex.prmtop procomplex.inpcrd
#The file cannot be saved, you know the amino acid residues in the small peptide (not protein) can not be recognized by the AMBER anymore (But before dokcing, it can be load into xleap without errors.)
#But when the protein (Receptor) was saved as pdb form and the ligand (small peptide) was saved as mol2 in sybyl and loaded them separately in to the AMBER, I found there was no errors with this ligand anymore.
b = loadmol2 ligand.mol2
edit b #very good
saveamberparm b ligand.prmtop d.inpcrd
#File cannot be saved still, because of unknow atoms bond typesand unproper angles!
#So I want to use antechamber to produce the parameters laking in the ligand using antechamber, but errors appears as follows:
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/home/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit
The atom number exceeds the MAXATOM, reallocate memory
#Thus I want to divide this mol2 form ligand into several segaments, so I can obtain all the prepin and frcmod files of the ligand, then I plan to load them into xleap.
#Ligand was divided in to 5 parts,named seg1.mol2 ,seg2.mol2, seg3.mol2 , seg4.mol2,seg5.mol2. There preppin and frcmod files as
seg1.prepin ,seg2.prein, seg3.prepin , seg4.prepin,seg5.mol2.
seg1.frcmod, seg2.frcmod, seg3.frcmod, seg4.frcmod, seg5.frcmod .
#By editing the prepin files, I named them as M_1, M_2,M_3, M_4,M_5. Then I load them to xleap as following:
loadamberprep seg1.prepin
loadamberfrcmod seg1.frcmod
loadamberprep seg5.prepin
loadamberfrcmod seg5.frcmod
list # I could find 5 new units M_1, M_2,M_3, M_4,M_5.were added in to the filed!
I want to use combine to combine them to one intact ligand.
c = combine{M_1, M_2,M_3, M_4,M_5}
edit c #In the xleap, I want to continue, link them and add atom types and charges. Unfortunately, there still lack of some angle errors! How can I solve these? Is there any references to obtain both the atom types, charges and angle parameter (especially?)
I blieve when the angle parameters are added I can obtain the intact ligand again!
Best Regards,
Rilei Yu


Rilei Yu

--- 09年3月29日,周日, David A. Case <> 写道:

发件人: David A. Case <>
主题: Re: [AMBER] Load protein complex to Xleap (Combine)
收件人: "AMBER Mailing List" <>
日期: 2009年3月29日,周日,上午10:26


On Sun, Mar 29, 2009, Rilei Yu wrote:

> I ever came across a problem-when I docked small peptideswith anmino
> acid residues aranged between 12_20. You know, when I docked them in to
> the protein in sybyl, I found these peptides were not considered to be
> usual amino acid any more. So I have to load those small peptide in the
> mol2 form.

I'm lost here: when you say "load those small peptide", do you mean into
Sybyl?  For Amber, it would certainly be easier to use the loadpdb
command, and use the same force fields as we usually use for proteins.
If all you have are amino acids, there should be no reason to use
antehcamber at all.


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Received on Sun Mar 29 2009 - 01:18:59 PDT
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