Dear mailing list,
I am a new user of Relax and new to the field of dynamics as well. At the
moment I am trying to run the multimodel.py script myself, but am having
trouble getting relax to caluculate the m6 model. It will calculate the
m0 to m5 models, but then an error message comes up for model 6.
relax> pipe.create(pipe_name='m6', pipe_type='mf')
relax> sequence.read(file='sequence.out', dir=None, mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=2,
sep=None)
Opening the file 'sequence.out' for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1510 Ser None N
None 1511 Asn None N
None 1512 Glu None N
None 1513 His None N
None 1514 Asp None N
None 1515 Asp None N
None 1516 Cys None N
None 1517 Gln None N
None 1518 Val None N
None 1519 Thr None N
None 1520 Asn None N
None 1521 Pro None N
None 1522 Ser None N
None 1523 Thr None N
None 1524 Gly None N
None 1525 His None N
None 1526 Leu None N
None 1527 Phe None N
None 1528 Asp None N
None 1529 Leu None N
None 1530 Ser None N
None 1531 Ser None N
None 1532 Leu None N
None 1533 Ser None N
None 1534 Gly None N
None 1535 Arg None N
None 1536 Ala None N
None 1537 Gly None N
None 1538 Phe None N
None 1539 Thr None N
None 1540 Ala None N
None 1541 Ala None N
None 1542 Tyr None N
None 1543 Ser None N
None 1544 Glu None N
None 1545 Lys None N
None 1546 Gly None N
None 1547 Leu None N
None 1548 Val None N
None 1549 Tyr None N
None 1550 Met None N
None 1551 Ser None N
None 1552 Ile None N
None 1553 Cys None N
None 1554 Gly None N
None 1555 Glu None N
None 1556 Asn None N
None 1557 Glu None N
None 1558 Asn None N
None 1559 Cys None N
None 1560 Pro None N
None 1561 Pro None N
None 1562 Gly None N
None 1563 Val None N
None 1564 Gly None N
None 1565 Ala None N
None 1566 Cys None N
None 1567 Phe None N
None 1568 Gly None N
None 1569 Gln None N
None 1570 Thr None N
None 1571 Arg None N
None 1572 Ile None N
None 1573 Ser None N
None 1574 Val None N
None 1575 Gly None N
None 1576 Lys None N
None 1577 Ala None N
None 1578 Asn None N
None 1579 Lys None N
None 1580 Arg None N
None 1581 Leu None N
None 1582 Arg None N
None 1583 Tyr None N
None 1584 Val None N
None 1585 Asp None N
None 1586 Gln None N
None 1587 Val None N
None 1588 Leu None N
None 1589 Gln None N
None 1590 Leu None N
None 1591 Val None N
None 1592 Tyr None N
None 1593 Lys None N
None 1594 Asp None N
None 1595 Gly None N
None 1596 Ser None N
None 1597 Pro None N
None 1598 Cys None N
None 1599 Pro None N
None 1600 Ser None N
None 1601 Lys None N
None 1602 Ser None N
None 1603 Gly None N
None 1604 Leu None N
None 1605 Ser None N
None 1606 Tyr None N
None 1607 Lys None N
None 1608 Ser None N
None 1609 Val None N
None 1610 Ile None N
None 1611 Ser None N
None 1612 Phe None N
None 1613 Val None N
None 1614 Cys None N
None 1615 Arg None N
None 1616 Pro None N
None 1617 Glu None N
None 1618 Ala None N
None 1619 Gly None N
None 1620 Pro None N
None 1621 Thr None N
None 1622 Asn None N
None 1623 Arg None N
None 1624 Pro None N
None 1625 Met None N
None 1626 Leu None N
None 1627 Ile None N
None 1628 Ser None N
None 1629 Leu None N
None 1630 Asp None N
None 1631 Lys None N
None 1632 Gln None N
None 1633 Thr None N
None 1634 Cys None N
None 1635 Thr None N
None 1636 Leu None N
None 1637 Phe None N
None 1638 Phe None N
None 1639 Ser None N
None 1640 Trp None N
None 1641 His None N
None 1642 Thr None N
None 1643 Pro None N
None 1644 Leu None N
None 1645 Ala None N
None 1646 Cys None N
None 1647 Glu None N
None 1648 Gln None N
None 1649 Ala None N
None 1650 Thr None N
None 1651 Lys None N
None 1652 Glu None N
None 1653 His None N
relax> structure.read_pdb(file='structure.pdb', dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'structure.pdb' for reading.
Adding molecule 'structure_mol1' to model None (from the original molecule
number 1 of model None)
relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
file='R1.out', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R1.out' for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
file='R2.out', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file 'R2.out' for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
file='NOE.out', dir=None, mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2,
error_col=3, sep=None)
Opening the file 'NOE.out' for reading.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00017199999999999998, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m6', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
RelaxError: All parameters are fixed.
-------------------------------------------------------------------------------------------------------------------------------------------
Any ideas? Should I be setting the spin id? I don't understand why model
6 is the problem in particular.
I'd be very grateful if you could help me out - I feel a bit overwhelmed!
Maddy Strickland
(University of Bristol, 2nd year PhD)
[Fwd: Re: Relax]