AMBER Archive (2008)

Subject: RE: AMBER: Problems simulating a protein-ligand complex

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Jun 07 2008 - 00:15:32 CDT

Hi Sasha,

 

Okay, that is just weird... I suspect there is a parameter that is making something collapse onto another atom, perhaps a dodgy VDW radii. I assume all the test cases pass without problems.

 

Something to try.

 

Set Maxcyc=200, ncyc=200, ntpr=1 and ntwr=-1

 

This way you will be able to see every step in the mdout file. You will also get a restart file for every step. In this way you can look at the structure immediately before it turns to NaNs and see how it differs from th initial structure. This will hopefully identify which atom / region is causing the problems.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Sasha Buzko
Sent: Friday, June 06, 2008 4:40 PM
To: amber_at_scripps.edu
Subject: RE: AMBER: Problems simulating a protein-ligand complex

 

Ross,
The output is below. Thanks

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 9

| Run on 06/06/2008 at 16:09:26

  [-O]verwriting output

File Assignments:
| MDIN: min.in
| MDOUT: complex_min.out
| INPCRD: complex.inpcrd
| PARM: complex.prmtop
| RESTRT: complex_min.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile

Here is the input file:

Initial minimisation of our complex
&cntrl
  imin=1, maxcyc=1000, ncyc=400,
  cut=20, ntb=0, igb=1,
/

| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| SLOW_NONBLOCKING_MPI
| PUBFFT
| FFTLOADBAL_2PROC
| MKL

| New format PARM file being parsed.
| Version = 1.000 Date = 06/06/08 Time = 16:01:47
| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

NATOM = 2694 NTYPES = 17 NBONH = 1329 MBONA = 1388
NTHETH = 3017 MTHETA = 1881 NPHIH = 5748 MPHIA = 4591
NHPARM = 0 NPARM = 0 NNB = 14815 NRES = 168
NBONA = 1388 NTHETA = 1881 NPHIA = 4591 NUMBND = 59
NUMANG = 119 NPTRA = 52 NATYP = 43 NPHB = 0
IFBOX = 0 NMXRS = 46 IFCAP = 0 NEXTRA = 0
NCOPY = 0

Implicit solvent radii are modified Bondi radii (mbondi)
--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 1, ntb = 0, igb = 1, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 20.00000, intdiel = 1.00000
     saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
     gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
     rdt = 0.00000, rgbmax = 25.00000
     alpb = 0
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Energy minimization:
     maxcyc = 1000, ncyc = 400, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
begin time read from input coords = 0.000 ps

Number of triangulated 3-point waters found: 0
| Dynamic Memory, Types Used:
| Reals 81794
| Integers 252050

| Running AMBER/MPI version on 2 nodes

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -6.8120E+03 1.3612E+01 2.1864E+02 H42 2691

BOND = 361.7247 ANGLE = 397.1223 DIHED = 1628.3352
VDWAALS = -1261.3284 EEL = -11082.6784 EGB = -2549.3611
1-4 VDW = 700.0442 1-4 EEL = 4994.1524 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
     50 -7.7370E+03 8.4612E-01 1.9291E+01 PB 2656

BOND = 86.0923 ANGLE = 347.5428 DIHED = 1607.9732
VDWAALS = -1480.4067 EEL = -11036.0858 EGB = -2588.3621
1-4 VDW = 595.7157 1-4 EEL = 4730.5444 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    100 -7.8256E+03 6.4938E-01 1.8211E+01 CG 1860

BOND = 95.2522 ANGLE = 376.9760 DIHED = 1605.2109
VDWAALS = -1506.3884 EEL = -11062.2867 EGB = -2567.6875
1-4 VDW = 572.7459 1-4 EEL = 4660.5666 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    150 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = 0.0000
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    200 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = 0.0000
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    250 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = 0.0000
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    300 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = 0.0000
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    350 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = 0.0000
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    400 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = 0.0000
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

                    FINAL RESULTS

   NSTEP ENERGY RMS GMAX NAME NUMBER
    421 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = 0.0000
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000

     ***** REPEATED LINMIN FAILURE *****
--------------------------------------------------------------------------------
   5. TIMINGS
--------------------------------------------------------------------------------

| NonSetup CPU Time in Major Routines, Average for All Tasks:
|
| Routine Sec %
| ------------------------------
| DataDistrib 0.68 0.14
| Nonbond 493.96 99.54
| Bond 0.02 0.00
| Angle 0.17 0.03
| Dihedral 1.39 0.28
| Shake 0.00 0.00
| Other 0.04 0.01
| ------------------------------
| Total 496.26

| Generalized Born CPU Time, Average for All Tasks:
|
| Routine Sec %
| ------------------------------------
| Radii Calc 37.90 7.64
| Diagonal Calc 263.50 53.10
| Off Diagonal Calc 192.32 38.75
| Radii Distrib 0.24 0.05
| ---------------------------------
| Total 493.96 99.54

| Master Setup CPU time: 0.03 seconds
| Master NonSetup CPU time: 496.69 seconds
| Master Total CPU time: 496.72 seconds 0.14 hours

| Master Setup wall time: 0 seconds
| Master NonSetup wall time: 261 seconds
| Master Total wall time: 261 seconds 0.07 hours

On Fri, 2008-06-06 at 16:34 -0700, Ross Walker wrote:

Hi Sasha,

 

Can you post the output file from the minimization? You probably have two atoms sitting on top of each other or very close.

 

All the best

Ross

 

From:owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Sasha Buzko
Sent: Friday, June 06, 2008 4:13 PM
To: amber_at_scripps.edu
Subject: RE: AMBER: Problems simulating a protein-ligand complex

 

Hi Ross,
thank you for the detailed instructions (although I'm trying to use GB and avoid having to add explicit solvent).

I did get a complex with the correct position of the ligand (used Sirius to check the prmtop/inpcrd). But at the stage of minimization I run into NaN values for all energies after about 100 steps (in the minimization out file). Not sure whether it's missing parameters or something else.. frcmod file had the following:

IMPROPER
c3-cc-na-cc 1.1 180.0 2.0 Using default value
h5-na-cc-nd 1.1 180.0 2.0 Using default value
c -cc-cd-nd 1.1 180.0 2.0 Using default value
cd-nc-c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
na-nc-cd-nh 1.1 180.0 2.0 Using default value
cd-hn-nh-hn 1.1 180.0 2.0 Using default value
cc-cd-na-hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
cd-na-cc-na 1.1 180.0 2.0 Using default value

But again, I'm not sure what could cause the issue with NaN values. Since the ligand is a triphosphate, I set its charge to -3 (using -nc -3 flag for antechamber). In any event, I'm a bit low on possible causes..
Can you think of anything in this regard?

Thanks again

Sasha

On Fri, 2008-06-06 at 15:55 -0700, Ross Walker wrote:

 
 
Hi Sasha,
 
I would do something along the lines of the following:
 
1) open protein pdb in a text editor and remove the END (at the end) and just make sure there is a ter card there. Also remove any connectivity data.
 
2) open the ligand pdb file and remove anything prior to the first atom definition. Go to the end and remove everything past the last atom definition and just add an END card.
 
3) cp protein pdb to complex.pdb
   Cat ligand pdb >> complex.pdb
 
4) load leap
   Source leaprc.ff99SB
   Source leaprc.gaff
   Loadamberprep ligand.prep
   Loadamberparams ligand.frcmod
   Foo = loadpdb complex.pdb
   Solvateoct foo TIP3PBOX 10.0
   Saveamberparm foo prmtop inpcrd
 
I hope that makes sense and is what you actually want to do I.e make a prmtop and inpcrd for the solvated complex.
 
All the best
Ross
 
 
 
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Sasha Buzko
Sent: Friday, June 06, 2008 3:16 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Problems simulating a protein-ligand complex
 
Thank you, David.
 
With hydrogens added in another application, the antechamber part worked.
 
But another issue appears when I combine the protein structure with the antechamber output in xleap. The ligand is loaded as a prepin file, followed by its frcmod with missing parameters. Then I load the pdb file of the protein and use complex = combine { protein GNP }, where GNP is the name of the residue assigned to the ligand. However, the ligand ends up being shifted in space far from the protein, even though the initial coordinates corresponded to the complex.. I assume that it's the result of the intermediate operations.. but is there a way to combine the two entities into the original complex?
 
Thanks for any advice
 
Sasha
 
 
 
 
On Fri, 2008-06-06 at 11:59 -0700, David A. Case wrote:
 
On Fri, Jun 06, 2008, Sasha Buzko wrote:
>
> The structure has correct connectivity and came directly from a PDB
> file. Since the ligand PDB file is not that large, I'm pasting it below.
> Thank you for any suggestions.
 
You don't have any hydrogen atoms in your input structure. Antechamber
doesn't know how to add hydrogens...you need to draw them in by hand, or
use some other model building program to add all of the hydrogens.
 
...hope this helps...dac
 
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu
 
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu