Dear Jason,
Many thanks for your help. I have one more question to do with the layout
of the input.
My input currently reads:
Restrainted initial optimisation of intermediate for adiabatic mapping
&cntrl
imin=1, ncyc=20, maxcyc=200,
ntb=0, cut=99.0,
ibelly=1,
/
Moveable atoms
RES 8 8 12 12 27 64 66 66 68 69 80 80
RES 83 84 91 91 95 95 98 98 103 115 123 123
RES 130 132 136 136 138 138 150 150 154 154
RES 156 156 161 161 174 174 239 239 245 245 251 251
RES 257 257 265 265 314 315 348 348 371 371 394 394 404 404
RES 477 477 515 515 538 538 569 569 578 578 595 596 667 667
RES 677 677 679 680 683 683 698 698 771 771 779 779 798 798
RES 820 820 826 826 849 849 886 886 894 894 900 900 903 903 913 913
RES 921 922 960 960 963 963 990 990 1004 1004 1009 1009 1026 1026
RES 1029 1029 1036 1036 1047 1047 1051 1051 1056 1056 1092 1092 1113 1113
RES 1116 1116 1119 1119 1126 1127 1133 1133 1138 1138 1170 1171 1173 1173
RES 1177 1177 1188 1188 1195 1195 1204 1204 1210 1210 1213 1213 1217 1217
RES 1231 1231 1244 1244 1246 1246 1265 1266 1269 1269 1271 1271 1274 1274
RES 1284 1284 1288 1288 1294 1294 1301 1301 1310 1310 1318 1318 1324 1324
RES 1330 1330 1332 1332 1336 1336 1340 1340 1344 1344 1355 1355 1363 1364
RES 1382 1382 1385 1385 1393 1393 1399 1400 1402 1402 1409 1409 1415 1415
RES 1443 1443 1447 1448 1450 1451 1469 1469 1475 1475 1480 1480 1482 1482
RES 1488 1488 1493 1493 1500 1500 1505 1505 1507 1507 1511 1511 1528 1528
RES 1530 1530 1538 1538 1550 1550 1559 1559 1566 1566 1569 1569 1574 1575
RES 1596 1596 1604 1604 1612 1612 1635 1635 1662 1662 1673 1673 1692 1692
RES 1694 1694 1700 1700 1706 1706 1722 1722 1733 1733 1745 1745 1747 1747
RES 1752 1752 1783 1784 1811 1811 1826 1826 1834 1834 1845 1845 1851 1851
RES 1856 1856 1858 1858 1868 1868 1871 1871 1873 1873 1875 1875 1887 1887
RES 1905 1906 1920 1920 1924 1924 1932 1932 1942 1942 1945 1945 1949 1950
RES 1958 1958 1963 1963 1965 1965 1967 1967 1973 1973
END
END
nmropt=1,
ifqnt=1,
&qmmm
qmmask='.1962-1998,541-547,778-783',
qmcharge=-2,
qm_theory='DFTB',
qmshake=0,
qm_ewald=1, qm_pme=1,
writepdb=1,
lnk_dis=1.09,
lnk_method=1,
lnk_atomic_no=1,
/
&end
&wt
type='END',
&end
DISANG=rc_1.4_5.0.con
This calculation runs, however, the nmropt=1 and ifqnt=1 flags are ignored
(therefore no restraint or QM region allocated).
To try and solve this I put these flags before but then this just causes an
error too.
if nmropt=1 flag before ibelly:
*At line 143 of file rgroup.F90 (unit = 5, file = 'initial_opt.i')*
*Fortran runtime error: Read past ENDFILE record*
if ifqnt=1 flag before ibelly:
error in output
*rfree: End of file on unit 5*
if both before ibelly flag
error in output
*rfree: End of file on unit 5*
What should be the correct format / order of the above input file so all
the flags are read correctly?
Many thanks,
Mike
On 18 October 2013 19:05, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Oct 18, 2013 at 1:35 PM, Mike Limb <mikeallimb.gmail.com> wrote:
>
> > Dear Jason,
> >
> > Many thanks for your useful reply.
> >
> > I found a mask specification that allowed me to freeze all the atoms I
> > wanted. This was done with the command:
> >
> > bellymask=(!.1962-1998,541-547,778-783 < :10.0)
> >
>
> bellymask selects atoms that can move, not atoms that are fixed. This will
> fix all residues within 10 angstroms of your atom selection and allow
> everything else to move. I don't think this is what you want, right?
>
>
> >
> > this command allows me to freeze all residues that are within 10 A of the
> > QM region (which consists of atoms 1962-1998,541-547,778-783 ).
> >
> > With this setup I then performed a two dimensional QM MM scan (adiabatic
> > mapping) with an x_series consisting of a distance restraint (between
> atom
> > 782 to 1991) from 1.4 to 3.3 A and y_series consisting of a distance
> > restraint (1991 to 1993) from 4.1 to 1.4 A, thus generating a potential
> > energy surface.
> >
> > On analysis of the results I noticed that there were large
> discontinuities
> > in the energies that I had calculated.
> >
> > Inspection of my output files revealed that this was most likely due to
> the
> > fact that the region that fell within the belly mask restraint moved as
> the
> > size of the QM region changed during the reaction. As a result I was
> > getting inconsistencies in the size of my MM region (and frozen region)
> as
> > the scan progressed and hence jumps in the total energy.
> >
> > I though that one way to solve this problem could be to use the
> positional
> > restraints with the restraint mask:
> >
> > restraintmask=':* & (!.1962-1998,541-547,778-783 < :10.0)',
> >
>
> The :* is redundant here.
>
>
> >
> > and then using a refc structure, however, upon testing it seems that the
> > atoms that are included in the restraint are still selected using the
> > coordinate file that is read in at the beginning of the optimisation and
> > therefore the same problem of a changing frozen region still remains.
>
>
> > Consequently, I believe my only option left it to use the Group selection
> > detailed in Appendix B. Upon attempting this I don't understand the
> > documentation or the example that is given and how I can use the group
> > selection to allow me to select the residues that I would like to fix in
> my
> > optimisations (a list of which are attached).
> >
> > As a result I was wondering if you could give me some guidance how I
> could
> > do a setup of this type.
> >
> > eg say I had a ligand (resid 1) and surrounded by a two solvation layers
> of
> > water the first consisting of residues 2-10 and the second consisting of
> > 11-30.
> >
> > How could I use the group selection to tell sander during the
> optimisation
> > to do a QM optimisation of the ligand, MM on the rest of the system, *BUT
> > freezing the coordinates of the second solvation shell by specifying
> them
> > by the residue number using the group selection. *
> >
>
> Your QM region should be specified the same way (i.e., with atom numbers or
> a mask). To fix residues 11 through 30 using belly and the GROUP input, it
> would look something like this:
>
> &cntrl
> ...your variables here...
> ibelly=1,
> /
> Movable atoms
> RES 2 10
> END
> END
>
> This will allow residues 2 through 10 to move. You can alternatively
> specify atom numbers and ranges using "ATOM" instead of "RES". You can
> specify at most 7 residue or atom ranges per line, but can specify as many
> lines as you want. Also, you must specify _ranges_. If you want just 1
> residue, you need to specify it as a range (e.g., "RES 1 1").
>
> Another example:
>
> &cntrl
> ... your variables here...
> ibelly=1,
> /
> Movable atoms
> RES 1 10 20 30 35 35 37 37 39 39 50 58 60 72
> RES 80 80 82 82 84 84 86 86 88 88 90 90 92 92
> END
> END
>
> The above will allow residues 1 through 10, 20 through 30, 35, 47, 49, 50
> through 58, 60 through 72, 80, 82, 84, 86, 88, 90, and 92 to move. I don't
> know if there is a limit to how many lines you can specify, but I don't
> think there is.
>
> Keep in mind, belly selections and restraint selections are inverse
> compared to each other. Belly selections indicate atoms that can move
> while restraint selections indicate atoms that are restrained.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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>
--
Mike Limb
PhD Candidate
SCI Scholar 2013-2016 *http://www.soci.org*
Supervisor: Prof. Adrian Mulholland
Centre for Computational Chemistry
School of Chemistry
University of Bristol
*ml7684*.bristol.ac.uk<Adrian.Mulholland.bristol.ac.uk>
Bristol BS8 1TS
http://www.chm.bris.ac.uk/pt/ajm/Site/Home.html
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at UoB
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Received on Tue Oct 22 2013 - 04:00:03 PDT
