AMBER Archive (2006)

Subject: AMBER: MD and MMPBSA

From: alexandra.marques_at_fc.up.pt
Date: Wed Mar 08 2006 - 22:29:23 CST

Dear amber users,

I want to calculate the free energy of binding of a tetrameric protein
complexed
with a ligand (each monomer contains a ligand molecule), by using the MMPBSA
method. I have some basic questions:

1-I think leap is not numbering the water residues correctly. The complex has
1024 residues and leap added 13992 water residues. In the pdb file
created from
the crd and top files, after the residue 9999, the residues numbering
restart in
0. This leads to some residues having repeated numbers, although the atom
numbers are correct. Ambmask recognize only the residues numbered until 9999;
the others are assigned with a xxxx. Does anyone know what is going wrong and
whether this may affect the calculations?

REMARK
ATOM 1 N SER 1 28.315 52.323 72.575
ATOM 2 H1 SER 1 27.792 51.554 72.999
ATOM 3 H2 SER 1 28.828 51.959 71.779
ATOM 4 H3 SER 1 27.666 53.028 72.239
ATOM 5 CA SER 1 29.226 52.904 73.562
ATOM 6 HA SER 1 29.696 53.770 73.106
ATOM 7 CB SER 1 28.457 53.384 74.808
ATOM 8 2HB SER 1 29.136 53.977 75.446
ATOM 9 3HB SER 1 27.649 54.029 74.493
ATOM 10 OG SER 1 27.925 52.315 75.578
ATOM 11 HG SER 1 27.154 51.916 75.132
ATOM 12 C SER 1 30.331 51.927 73.933
ATOM 13 O SER 1 30.178 50.708 73.904
ATOM 14 N VAL 2 31.472 52.490 74.301
ATOM 15 H VAL 2 31.603 53.489 74.226
ATOM 16 CA VAL 2 32.546 51.702 74.904
ATOM 17 HA VAL 2 32.541 50.708 74.472
ATOM 18 CB VAL 2 33.911 52.343 74.638
...
ATOM 15503 H45 MOL 1024 26.524 45.066 41.377
ATOM 15504 H46 MOL 1024 27.567 44.495 47.339
TER
ATOM 15505 Na+ Na+ 1025 30.198 60.390 26.381
TER
ATOM 15506 Na+ Na+ 1026 64.893 35.028 68.485
TER
ATOM 15507 Na+ Na+ 1027 44.365 50.780 52.014
TER
ATOM 15508 Na+ Na+ 1028 51.172 45.428 43.300
TER
ATOM 15509 O WAT 1029 47.892 46.635 103.114
ATOM 15510 H1 WAT 1029 47.613 46.445 104.041
ATOM 15511 H2 WAT 1029 48.867 46.503 103.211
TER
...
ATOM 42413 O WAT 9997 29.048 18.470 34.658
ATOM 42414 H1 WAT 9997 29.214 17.506 34.526
ATOM 42415 H2 WAT 9997 29.769 18.665 35.303
TER
ATOM 42416 O WAT 9998 30.765 18.864 36.697
ATOM 42417 H1 WAT 9998 30.662 19.738 37.155
ATOM 42418 H2 WAT 9998 30.098 18.351 37.215
TER
ATOM 42419 O WAT 9999 21.846 24.035 38.255
ATOM 42420 H1 WAT 9999 21.309 24.858 38.143
ATOM 42421 H2 WAT 9999 22.722 24.390 37.956
TER
ATOM 42422 O WAT 0 29.058 18.042 30.499
ATOM 42423 H1 WAT 0 28.984 17.066 30.349
ATOM 42424 H2 WAT 0 29.094 18.341 29.560
TER
ATOM 42425 O WAT 1 31.841 14.324 33.948
ATOM 42426 H1 WAT 1 31.970 14.419 32.975
ATOM 42427 H2 WAT 1 32.179 13.415 34.076
TER
ATOM 42428 O WAT 2 21.666 22.861 40.673
ATOM 42429 H1 WAT 2 21.324 23.577 41.227
ATOM 42430 H2 WAT 2 21.702 23.304 39.794
...
ATOM 57467 O WAT 5015 47.434 49.404 -5.306
ATOM 57468 H1 WAT 5015 48.257 49.074 -5.752
ATOM 57469 H2 WAT 5015 46.886 48.588 -5.393
TER
END

2- I have some doubts about the restraints used in minimizations and
MD. I want
to perform the minimization (explicit solvent) in three steps: first to
hydrogens and solvent, second to lateral chains and the last to all.
What force
constant value one´s shall use? I am confused with that because some tutorials
use 500, while others 5000. Is it better to come back to restraint the
hydrogens together with solvent in the MD equilibration phase? I am
asking that
because I saw a tutorial, available in the internet, in which that was done.

3- I also have a doubt about the initial temperature (temp0) value that one´s
shall use in the equilibration phase. I saw some tutorials in which
temp0=0 but
in others, temp0=300.0 What shall be used?
My md.in file for equilibration phase is:

&cntrl
  imin = 0, irest=0, ntx=1,
  nstlim=1000, dt=0.002, scee = 1.2, nrespa=2,
  ntt=3, gamma_ln=1.0, tempi=0.0, temp0=300.0,
  ntb = 1, ntp=0,
  ntc=2, ntf=2,
  ntr = 1,
  ntwe=100, ntwx=100, ntpr=200,
  restraint_wt = 50.0
  restraintmask='!:WA= & !@H=',
  cut = 10.0
/

4- Can I use the MMPBSA method after a minimisation or is it absolutely
necessary to perform a MD first? How can I do that?

Best regards
Alexandra

-------------------------------------------------------------
A FCUP utiliza o sistema de webmail Horde/IMP (www.horde.org)

Visite: http://www.fc.up.pt/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu