Dear AMBER users:
I hope that this was not answered before but I did not find anything in
the AMBER mailing list achive.
I try to generate parameters for a modifide UTP with antechamber. When
all phosphate groups are completely deprotonated, I see a proton
transfer from the sugar ring to the terminal phospate group in sqm.out.
Even if this might be a reasonable reaction in vacuo, the obtained
partial charges are completely useless, since they correspond to another
"tautomer". Is it possible to just use the non-optimized structure for
the calculation of the partial charges or is there a better way to do it?
I also tried to get parameters for UTP with one proton attached to the
terminal phosphate group. Here sqm give a reasonable structure and the
parameterization ends without errors. When I, however, use these
parameters in an energy minimization, the proton gets very close to one
phosphorus and the electrostatic energy approaches -inf. In contrast,
the VDW energy does not change at all and, thus, it seem that VDW
parameters are missing in the input files. Below are the corresponding
mol2 and frcmod files from antechamber and the leap.in file.
Thank you very much.
Thomas
.<TRIPOS>MOLECULE
LIG#
42 43 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C01 -9.0320 -31.5650 11.1630 cc 1 LIG# -0.382200
2 C02 -9.3870 -32.5860 10.1920 cd 1 LIG# 0.100600
3 C07 -9.7670 -31.4330 12.4210 c 1 LIG# 0.721700
4 N03 -10.4740 -33.4250 10.5130 n 1 LIG# -0.345000
5 N06 -10.8580 -32.3250 12.6790 n 1 LIG# -0.601500
6 O08 -9.4550 -30.5970 13.2810 o 1 LIG# -0.700500
7 C04 -11.2760 -33.3380 11.7490 c 1 LIG# 0.803500
8 C09 -10.8080 -34.3260 9.4770 c3 1 LIG# 0.285500
9 H1 -11.3660 -32.2360 13.5710 hn 1 LIG# 0.319500
10 O05 -12.2380 -34.0410 12.0340 o 1 LIG# -0.690500
11 C10 -9.8930 -35.4280 9.2560 c3 1 LIG# 0.129100
12 O13 -12.0200 -34.9580 9.6660 os 1 LIG# -0.452600
13 C11 -10.6430 -36.2020 8.3050 c3 1 LIG# 0.104100
14 O29 -8.7670 -34.8550 8.7030 oh 1 LIG# -0.650800
15 C12 -12.0540 -35.9180 8.6480 c3 1 LIG# 0.109100
16 O28 -10.3940 -35.7200 7.0490 oh 1 LIG# -0.633800
17 C14 -12.7740 -37.1540 9.0670 c3 1 LIG# 0.180400
18 O15 -12.6110 -37.6130 10.3620 os 1 LIG# -0.601200
19 P16 -11.9680 -39.0010 10.7100 p5 1 LIG# 1.465700
20 N19 -10.2980 -38.9350 10.6110 n3 1 LIG# -0.989400
21 O18 -12.5840 -40.0470 9.8190 o 1 LIG# -0.870500
22 O17 -12.2420 -39.3960 12.1250 o 1 LIG# -0.870500
23 P20 -9.5640 -40.1360 9.7170 p5 1 LIG# 1.627700
24 H2 -9.7550 -38.1940 11.0760 hn 1 LIG# 0.399800
25 O21 -10.0020 -39.8980 8.3190 o 1 LIG# -0.921500
26 O22 -8.0580 -39.9070 9.7630 o 1 LIG# -0.921500
27 O23 -9.9440 -41.5600 10.1620 os 1 LIG# -0.843800
28 P24 -8.8850 -42.6320 10.4370 p5 1 LIG# 1.593800
29 O25 -9.0130 -43.7270 9.4650 o 1 LIG# -0.895000
30 O26 -7.5340 -42.0160 10.4930 o 1 LIG# -0.895000
31 O27 -9.1940 -43.2590 11.7180 oh 1 LIG# -0.813400
32 H3 -10.0700 -43.6460 11.6480 ho 1 LIG# 0.425000
33 H4 -10.8620 -33.7530 8.5390 h2 1 LIG# 0.099700
34 H5 -9.6870 -35.9870 10.1810 h1 1 LIG# 0.114700
35 H6 -10.4250 -37.2760 8.3980 h1 1 LIG# 0.127700
36 H7 -12.5560 -35.5040 7.7610 h1 1 LIG# 0.052700
37 H8 -12.4570 -37.9880 8.4230 h1 1 LIG# 0.034200
38 H9 -13.8560 -36.9930 8.9520 h1 1 LIG# 0.034200
39 H10 -8.2100 -30.8910 10.9520 ha 1 LIG# 0.180000
40 H11 -8.8410 -32.6980 9.2620 h4 1 LIG# 0.265000
41 H12 -8.9830 -33.9350 8.6050 ho 1 LIG# 0.488000
42 H13 -11.1650 -35.2120 6.8240 ho 1 LIG# 0.419000
.<TRIPOS>BOND
1 1 2 2
2 1 3 1
3 1 39 1
4 2 4 1
5 2 40 1
6 3 5 1
7 3 6 2
8 4 7 1
9 4 8 1
10 5 7 1
11 5 9 1
12 7 10 2
13 8 11 1
14 8 12 1
15 8 33 1
16 11 13 1
17 11 14 1
18 11 34 1
19 12 15 1
20 13 15 1
21 13 16 1
22 13 35 1
23 14 41 1
24 15 17 1
25 15 36 1
26 16 42 1
27 17 18 1
28 17 37 1
29 17 38 1
30 19 18 1
31 19 20 1
32 19 21 1
33 19 22 1
34 23 20 1
35 20 24 1
36 23 25 1
37 23 26 1
38 23 27 1
39 28 27 1
40 28 29 1
41 28 30 1
42 28 31 1
43 31 32 1
.<TRIPOS>SUBSTRUCTURE
1 LIG# 1 TEMP 0 **** **** 0 ROOT
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
c -cd-cc-ha 1.1 180.0 2.0 Using
default value
cc-h4-cd-n 1.1 180.0 2.0 Using
default value
cc-n -c -o 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
c -c3-n -cd 1.1 180.0 2.0 Using
default value
c -c -n -hn 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
n -n -c -o 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
NONBON
source leaprc.ff12SB
source leaprc.gaff
loadAmberParams MURU_CM04_ligand1_LIG1_0_bindmatch_ante.frcmod
loadAmberPrep /home-link/cpaex01/INPHARMA-workflow/metals.prp
loadAmberParams /home-link/cpaex01/INPHARMA-workflow/metals.dat
loadAmberParams frcmod.tip4pew
loadAmberParams frcmod.ionsjc_tip4pew
LIG = loadmol2 MURU_CM04_ligand1_LIG1_0_bindmatch_ante.mol2
XXX = loadPdb MURU_CM04_complex_bindmatch_amber.pdb
saveAmberParm XXX MURU_CM04_complex.top MURU_CM04_complex.xyz
quit
--
________________________________________________________________________________
Dr. Thomas E. Exner
Theoretische Pharmazeutische Chemie & Biophysik
Lehrstuhl Pharmazeutische Chemie
Pharmazeutisches Institut
Eberhard Karls Universität Tübingen
Auf der Morgenstelle 8 (Haus B)
72076 Tübingen
Germany
Tel.: +49-(0)7071-2976969
Mobil: +49-(0)171-3807485
Fax: +49-(0)7071-295637
E-Mail: Thomas.Exner[at]uni-tuebingen.de
Fachbereich Chemie und Zukunftskolleg
Universität Konstanz
78457 Konstanz
Germany
Tel.: +49-(0)7531-882015
Fax: +49-(0)7531-883587
E-Mail: Thomas.Exner[at]uni-konstanz.de
________________________________________________________________________________
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Received on Thu Mar 27 2014 - 09:00:04 PDT
