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AMBER Archive (2009)Subject: [AMBER] Docking with Amber
From: Jordan, Brad (jbjordan_at_amgen.com)
Hi all - I'm attempting to dock a small molecule to a protein binding pocket using intermolecular NOE restraints. I'm having some problems and was hoping someone could help out. Here is what I've done so far:
1. created a .mol2 file of the ligand and used antechamber to get it to the correct format. I have generated the files ligand.frcmod and ligand.prepi
Source leaprc.ff99
I then use the prmtop and coordinate file as input to minimization and MD runs. First, I just try a simple minimization without restraints and get the following erroneous output.
&cntrl
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| Flags:
| Memory Use Allocated Used
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General flags:
Nature and format of input:
Nature and format of output:
Potential function:
Frozen or restrained atoms:
Energy minimization:
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
GROUP 1 HAS HARMONIC CONSTRAINTS 1.00000
Number of atoms in this group = 0
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begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
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NSTEP ENERGY RMS GMAX NAME NUMBER
BOND = 101.3867 ANGLE = 231.9497 DIHED = 1194.9679
NSTEP ENERGY RMS GMAX NAME NUMBER
BOND = nan ANGLE = nan DIHED = 553.6600
NSTEP ENERGY RMS GMAX NAME NUMBER
BOND = nan ANGLE = nan DIHED = 553.6600
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
BOND = nan ANGLE = nan DIHED = 553.6600
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
BOND = nan ANGLE = nan DIHED = 553.6600
***** REPEATED LINMIN FAILURE *****
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| Highest rstack allocated: 22462
| Setup wallclock 0 seconds
I would appreciate any ideas as to what I'm doing wrong.
Thanks in advance.
Brad
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