[gmx-users] Re: gmx-users digest, Vol 1 #1248 - 7 msgs
Jorge Hernanez Fernandez
jorgehf at cbi.cnptia.embrapa.br
Tue Feb 3 20:29:01 CET 2004
Dear GMXers!:
Im using GMX for a year, and actually interested in the free energy
evaluation in a Enzyme-inhibitor system. My protein is a metallo (Zn) and
inhibitor is a small peptide.
The central problem is that pdb2gmx read my system as a one whole
protein, and am not able to create a working index to obtain my peptide as a
separate Ener-group. Make_ndx is working find (I think
.):
>
0 System : 61990 atoms
1 Protein : 6152 atoms
2 Protein-H : 4793 atoms
3 C-alpha : 588 atoms
4 Backbone : 1764 atoms
5 MainChain : 2354 atoms
6 MainChain+Cb : 2911 atoms
7 MainChain+H : 2911 atoms
8 SideChain : 3241 atoms
9 SideChain-H : 2439 atoms
10 Prot-Masses : 6152 atoms
11 Non-Protein : 55838 atoms
12 Zn : 1 atoms
13 SOL : 55827 atoms
14 Na : 10 atoms
15 Other : 55838 atoms
16 BDK : 105 atoms XXX new formed inhibitor group!!!!XX
>
For group 16:
>
[ BDK ]
6049 6050 6051 6052 6053 6054 6055 6056 6057 6058 6059 6060 6061 6062 6063
6064 6065 6066 6067 6068 6069 6070 6071 6072 6073 6074 6075 6076 6077 6078
6079 6080 6081 6082 6083 6084 6085 6086 6087 6088 6089 6090 6091 6092 6093
6094 6095 6096 6097 6098 6099 6100 6101 6102 6103 6104 6105 6106 6107 6108
6109 6110 6111 6112 6113 6114 6115 6116 6117 6118 6119 6120 6121 6122 6123
6124 6125 6126 6127 6128 6129 6130 6131 6132 6133 6134 6135 6136 6137 6138
6139 6140 6141 6142 6143 6144 6145 6146 6147 6148 6149 6150 6151 6152 6153
>
but the next problem appears when running grompp:
>
grompp -f full.mdp -c XX.gro -p XX.top -o XX.tpr -n
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1125 of the 1326 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for Protein_C 1 XXXXX Zn ion !!!!! XXXXX
turning all bonds into constraints...
Excluding 3 bonded neighbours for Protein_B 1 XXXXXX inhibitor !!! XXXXXXX
turning all bonds into constraints...
Excluding 1 bonded neighbours for SOL 18609
turning all bonds into constraints...
Excluding 1 bonded neighbours for Na 10
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 312 K
renumbering atomtypes...
converting bonded parameters...
# ANGLES: 36904
# PDIHS: 16190
# IDIHS: 16800
# LJ14: 34023
# CONSTR: 18888
# SETTLE: 37218
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Fatal error: Atom 6048 in multiple T-Coupling groups (16 and 0)
>
As we see, the BDK group start in the 6049 atom!!! My XX.gro file is :
>
.
579GLN N 6035 2.573 4.498 2.037
579GLN H 6036 2.668 4.466 2.031
579GLN CA 6037 2.489 4.440 2.143
579GLN CB 6038 2.447 4.545 2.246
579GLN CG 6039 2.564 4.599 2.327
579GLN CD 6040 2.528 4.728 2.401
579GLN OE1 6041 2.435 4.743 2.480
579GLN NE2 6042 2.595 4.834 2.354
579GLN HE21 6043 2.655 4.805 2.279
579GLN HE22 6044 2.568 4.916 2.405
579GLN C 6045 2.371 4.355 2.095
579GLN O1 6046 2.355 4.341 1.961
579GLN O2 6047 2.292 4.300 2.191
580Zn ZN 6048 4.740 4.218 4.527 XXXXX problem is here (Zn)!!!XXX
581ARG N 6049 4.409 5.246 5.963
581ARG H1 6050 4.485 5.296 5.921
581ARG H2 6051 4.341 5.311 5.997
581ARG H3 6052 4.444 5.191 6.039
581ARG CA 6053 4.347 5.158 5.863
581ARG CB 6054 4.446 5.057 5.804
581ARG CG 6055 4.386 4.961 5.700
581ARG CD 6056 4.487 4.870 5.629
581ARG NE 6057 4.553 4.786 5.730
581ARG HE 6058 4.491 4.733 5.788
581ARG CZ 6059 4.683 4.769 5.757
581ARG NH1 6060 4.772 4.843 5.690
>
and my full.mdp is :
>
;
title = Prot-Inhib MD
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 50000 ; total 100 ps.
nstcomm = 1
nstxout = 500
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is off in two groups
Tcoupl = berendsen
tc-grps = Protein Zn SOL Na BDK
tau_t = 0.1 0.1 0.1 0.1 0.1
ref_t = 312 312 312 312 312
; Energy monitoring
energygrps = Protein BDK SOL
; Isotropic pressure coupling is on
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 312 K.
gen_vel = yes
gen_temp = 312.0
gen_seed = 173529
>
My Zn is contacting inhibitor (but non covalent!!). The problem
persists in ffgmx and ffoplsaa, and for index formed from .gro and .pdb files.
Any help is very welcome!!!
Sorry for long mail but is my last coin!!!:
Dr. Jorge H.F.
--
== Dr. JORGE HERNANDEZ FERNANDEZ ==
===== Lab. de Biofisica e Bioquimica =====
===== CAT-CEPID - Instituto Butantan =====
====== Ave Vital Brasil, 1500 S.P. ======
==== S.B.I.- EMBRAPA - BioInformatica ====
C.p. 6041 Cidade Universitária "Zeferino Vaz"
===== Barão Geraldo Campinas S.P. ======
=========== 13080-970 ==============
Tel: 0XX19-37895828
Cell: 0XX19-91336950
--
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