-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtleap_dna_protocol.py
79 lines (66 loc) · 5.12 KB
/
tleap_dna_protocol.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
tleap protocol ####################################################################################################################
Inspired by https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/
use tleap to prepare your pdb file in the correct amber format:
module purge
module load cpu/0.17.3b gcc/10.2.0/npcyll4 openmpi/4.1.3/oq3qvsv amber/22
tleap -f $AMBERHOME/dat/leap/cmd/leaprc.DNA.bsc1 #in this case this forcefield is for DNA
source leaprc.protein.ff14SB #I will consider this for proteins, only necessary if you will load proteins
source leaprc.water.tip3p #and water
#use the command >list
#this command will show all the elements that are considered in the system, for example check if all DNA bases are there, proteins that are in our system
#for example
> list
ACE AG AL ALA ARG ASH ASN ASP
Ag BA BR Be CA CALA CARG CASN
CASP CCYS CCYX CD CE CGLN CGLU CGLY
CHCL3BOX CHID CHIE CHIP CHIS CHYP CILE CL
CLEU CLYS CMET CO CPHE CPRO CR CS
CSER CTHR CTRP CTYR CU CU1 CVAL CYM
CYS CYX Ce Cl- Cr DA DA3 DA5
DAN DC DC3 DC4 DC5 DCN DG DG3
DG5 DGN DT DT3 DT5 DTN Dy EU
EU3 Er F FB3 FB3BOX FB4 FB4BOX FE
FE2 GD3 GLH GLN GLU GLY H3O+ HE+
HG HID HIE HIP HIS HOH HYP HZ+
Hf ILE IN IOD K K+ LA LEU
LI LU LYN LYS MEOHBOX MET MG MN
NA NALA NARG NASN NASP NCYS NCYX NGLN
NGLU NGLY NH4 NHE NHID NHIE NHIP NHIS
NI NILE NLEU NLYS NMABOX NME NMET NPHE
NPRO NSER NTHR NTRP NTYR NVAL Na+ Nd
O3P OP3 OPC OPC3BOX OPCBOX PB PD PHE
PL3 POL3BOX PR PRO PT Pu QSPCFWBOX RB
Ra SER SM SPC SPCBOX SPCFWBOX SPF SPG
SR Sm Sn T4E TB THR TIP3PBOX TIP3PFBOX
TIP4PBOX TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5 TPF
TRP TYR Th Tl Tm U4+ V2+ VAL
WAT Y YB2 ZN Zr dna1 frcmod14SB
>
dna1= loadpdb "1bna.pdb" #loads the pdb file
Loading PDB file: ./1bna.pdb
(starting new molecule for chain B)
total atoms in file: 566
Leap added 432 missing atoms according to residue templates:
432 H / lone pairs
saveamberparm dna1 1bna.prmtop 1bna.crdbox #this saves the coordinates and topology of the file
Warning: The unperturbed charge of the unit (-22.000000) is not zero.
Note: Ignoring the warning from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 164 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
WAT 80
)
(no restraints)
~/scripts/amber2bgf.pl [prmtop] [crdbox] [name_of_bgf_file_to_create]
~/scripts/amber2bgf.pl 1bna.prmtop 1bna.rst7 1bna.bgf #joins the files into a bgf file