Dear Amber Users/Authors,
I am performing TMD on a system, trying to simulate from open to close
conformer. During this simulation I would like to hold a salt bridge with a
distance restraint. And the salt bridge lies in a region on which TMD
restraints are applied.
Is it possible/okay (both technically) to combine Cartesian positional
restraints and TGTMD restraints in the same simulation.
And, also during the simulation, I have to use tgtfitmask, to calculate
rmsd after fitting the non-moving part of TMD.
ERROR:
ITGTMD: tgtrmsmask (and not tgtfitmask) should be specified if NTR=1
This is the TMD input file I am using.
############
Ubi targeted
MD
&cntrl
imin = 0, nstlim = 500000, dt =
0.004,
ntx = 1, ntt = 3, gamma_ln =
1.0,
ntc = 2, ntf = 2, ntb = 2,
ntp=1,
cut = 10.0, ig = -1, ntr =
1,
ntpr = 1000, ntwx = 1000, ntwr =
1000,
igb = 0, irest=0,
nmropt=1,tempi=300.0,
itgtmd=1,
tgtmdfrc=0.001,
tgtfitmask=":77-225.CA,N,C,O",
tgtrmsmask=":1-70.CA,N,C,O",
/
&wt
TYPE='TGTRMSD', istep1 = 0, istep2 =
50000,
value1 = 46.020, value2 =
45.0,
/
&wt
TYPE='TGTRMSD', istep1 =50001, istep2 =
60000,
value1 = 45.0, value2 =
45.0,
/
&wt
TYPE='TGTRMSD', istep1 = 60001, istep2 =
100000,
value1 = 45.0, value2 =
40.0,
/
&wt
TYPE='TGTRMSD', istep1 =100001, istep2 =
120000,
value1 = 40.0, value2 =
40.0,
/
&wt
TYPE='TGTRMSD', istep1 =120001, istep2 =
160000,
value1 = 40.0, value2 =
35.0,
/
&wt
TYPE='TGTRMSD', istep1 =160001, istep2 =
180000,
value1 = 35.0, value2 =
35.0,
/
&wt
TYPE='TGTRMSD', istep1 =180001, istep2 =
220000,
value1 = 35.0, value2 =
30.0,
/
&wt
TYPE='TGTRMSD', istep1 =220001, istep2 =
240000,
value1 = 30.0, value2 =
30.0,
/
&wt
TYPE='TGTRMSD', istep1 =240001, istep2 =
280000,
value1 = 30.0, value2 =
25.0,
/
&wt
TYPE='TGTRMSD', istep1 =280001, istep2 =
300000,
value1 = 25.0, value2 =
25.0,
/
&wt
TYPE='TGTRMSD', istep1 =300001, istep2 =
340000,
value1 = 25.0, value2 =
20.0,
/
&wt
TYPE='TGTRMSD', istep1 =340001, istep2 =
360000,
value1 = 20.0, value2 =
20.0,
/
&wt
TYPE='TGTRMSD', istep1 =360001, istep2 =
400000,
value1 = 20.0, value2 =
10.0,
/
&wt
TYPE='TGTRMSD', istep1 =400001, istep2 =
420000,
value1 = 10.0, value2 =
5.0,
/
&wt
TYPE='TGTRMSD', istep1 =420001, istep2 =
460000,
value1 = 5.0, value2 =
0.0,
/
&wt
TYPE='TGTRMSD', istep1 =460001, istep2 =
500000,
value1 = 0.0, value2 =
0.0,
/
&wt
type="END",
/
LISTOUT=POUT
DISANG=../Dest_res_prep/RST.dist
############
Distance Restraint file (created using makeDIST_RST):
#
# 40 GLU OE2 72 ARG NH2 4.0
&rst
ixpk= 0, nxpk= 0, iat= 634, -1, r1= 2.50, r2= 3.00, r3= 4.00, r4= 4.50,
rk2=0.0, rk3=20.0, ir6=1, ialtd=0,
igr2=1168,1169,
/
############
Best regards and many thanks in advance,
Aravind R
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Received on Tue Jan 22 2019 - 01:00:03 PST
