Hi,
I saw your ADP.prep. it doesn't have the coordinate or the connection between Mg2+ and other atom.
maybe your .prep it's wrong.
Best wish,
Kungking
________________________________
From: Tommaso Biagini <tommasobiagini.gmail.com>
Sent: Thursday, May 11, 2017 12:15 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MG angle parameter
thnks for the answer
this is my ADP.prep
adp INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 0 0 0.000 0.000 0.000 0.000
2 DUMM DU M 1 0 0 1.000 0.000 0.000 0.000
3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.000
4 O1B O3 M 3 2 1 1.000 90.000 180.000 -0.9552
5 PB P M 4 3 2 1.434 90.000 180.000 1.3672
6 O2B O3 E 5 4 3 1.574 107.490 -79.441 -0.9552
7 O3B O3 E 5 4 3 1.518 118.007 165.990 -0.9552
8 O3A OS M 5 4 3 1.599 113.374 180.000 -0.6346
9 PA P M 6 5 4 1.646 130.619 36.624 1.4929
10 O1A O2 E 7 6 5 1.504 109.212 -90.234 -0.9474
11 O2A O2 E 7 6 5 1.526 108.570 40.323 -0.9474
12 O5* OS M 7 6 5 1.585 97.173 157.726 -0.6579
13 C5* CT M 8 7 6 1.445 122.292 -66.317 0.0558
14 H50 H1 E 9 8 7 1.059 109.484 27.531 0.0679
15 H51 H1 E 9 8 7 1.059 109.437 -92.456 0.0679
16 C4* CT M 9 8 7 1.477 113.286 147.538 0.1065
17 H40 H1 E 16 9 8 1.059 105.768 -179.178 0.1174
18 O4* OS S 16 13 9 1.482 106.235 -62.889 -0.3548
19 C1* CT B 18 16 13 1.391 107.688 128.804 0.0394
20 H10 H2 E 19 18 16 1.059 109.468 91.228 0.2007
21 N9 N* S 19 18 16 1.552 105.091 -143.300 -0.0251
22 C8 CK B 21 19 18 1.388 123.797 33.434 0.2006
23 H80 H5 E 22 21 19 1.078 131.047 -3.389 0.1553
24 N7 NB S 22 21 19 1.384 108.967 176.598 -0.6073
25 C5 CB S 24 22 21 1.395 103.021 0.702 0.0515
26 C6 CA B 25 24 22 1.412 128.288 178.252 0.7009
27 N6 N2 B 26 25 24 1.333 125.907 -3.791 -0.9019
28 H60 H E 27 26 25 1.010 120.010 2.829 0.4115
29 H61 H E 27 26 25 1.009 120.014 -177.167 0.4115
30 N1 NC S 26 25 24 1.343 113.319 178.851 -0.7615
31 C2 CQ B 30 26 25 1.340 123.433 -1.664 0.5875
32 H2 H5 E 31 30 26 1.077 120.022 -177.875 0.0473
33 N3 NC S 31 30 26 1.377 125.379 2.123 -0.6997
34 C4 CB E 33 31 30 1.300 108.242 -0.035 0.3053
35 C3* CT M 16 13 12 1.484 117.051 57.581 0.2022
36 H30 H1 E 35 16 13 1.059 117.939 24.820 0.0615
37 O3* OH S 35 16 13 1.407 108.509 149.908 -0.6541
38 H3* HO E 37 35 16 0.967 109.470 163.254 0.4376
39 C2* CT M 35 16 13 1.607 102.425 -96.715 0.0670
40 H20 H1 E 39 35 16 1.059 115.086 78.119 0.0972
41 O2* OH S 39 35 16 1.398 114.943 -153.294 -0.6139
42 H2* HO E 41 39 35 0.967 109.456 -41.679 0.4186
IMPROPER
C8 C4 N9 C1*
C6 H60 N6 H61
N7 N9 C8 H80
N1 N3 C2 H2
C5 N1 C6 N6
LOOP CLOSING EXPLICIT
C1* C2*
C4 C5
C4 N9
DONE
STOP
this is the frcmod.phos:
# Modifications to the AMBER94 force field for polyphosphates
MASS
CT 12.01
OS 16.00
P 30.97
H1 1.008
O2 16.00
O3 16.00
BOND
CT-H1 340.000 1.090 from amber98
CT-OS 320.000 1.410
OS-P 230.000 1.61000
O2-P 525.000 1.480
O3-P 525.000 1.480 by analogy to O2
ANGLE
H1-CT-OS 50.000 109.500
H1-CT-H1 35.000 109.500
CT-OS-P 100.000 120.500
O2-P -O2 140.000 119.900
O3-P -O3 140.000 119.90 by analogy to O2
OS-P -O2 100.000 108.230
OS-P -O3 100.000 108.23 by analogy to O2
OS-P -OS 45.000 102.600
P -OS-P 12.685 150.000 J Comp Chem 2003, 24, 1016-1025
DIHE
H1-CT-OS-P 3 0.105 000.000 3.000 J Comp Chem
2003, 24, 1016-1025
O2-P -OS-CT 2 1.179 000.000 -3.000 J Comp Chem
2003, 24, 1016-1025
O2-P -OS-CT 2 -0.812 000.000 2.000 J Comp Chem
2003, 24, 1016-1025
CT-OS-P -OS 1 -1.560 0.0 1.0 J Comp Chem
2003, 24, 1016-1025
O2-P -OS-P 2 -0.709 0.0 2.0 J Comp Chem
2003, 24, 1016-1025
O3-P -OS-P 3 -0.255 0.0 3.0 J Comp Chem
2003, 24, 1016-1025
P -OS-P -OS 1 0.897 0.00 1.0 J Comp Chem
2003, 24, 1016-1025
NONBON
H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
O2 1.6612 0.2100 OPLS
O3 1.6612 0.2100 OPLS - by analogy to O2
CT 1.9080 0.1094 Spellmeyer
P 2.1000 0.2000 JCC,7,(1986),230;
OS 1.6837 0.1700 OPLS ether
This is the magnesium prep:
0 0 2
------magnesium--------------
MG
MG INT 0
CHANGE OMIT DU BEG
0.0
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.000
2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000
3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000
4 MG MG M 29.683 127.561 -18.450 2.00
DONE
STOP
and this is
Mg2+ vdw parameters from Magnesium Optimization Paper
MASS
MG 24.305 0.120 magnesium
NONB
MG 1.5545 0.00295 Allner et al. JCTC , 8, 1493-1502,
(2012)
I have already changed the name of atoms in accordance with those reported
in .prep files
the error seems something connected with angle parameters.
How can I set angle parameters for MG ion?
Thanks
2017-05-10 16:21 GMT+02:00 Elvis Martis <elvis.martis.bcp.edu.in>:
> Hi,
> Check the atom name for MG atom and check what is there in prep file
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<http://www.elvismartis.in>
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Tommaso Biagini [mailto:tommasobiagini.gmail.com]
> Sent: Wednesday, May 10, 2017 6:08 PM
> To: amber.ambermd.org
> Subject: [AMBER] MG angle parameter
>
> Dar all amber users,
>
> I want to simulate the complex with pdbid: 3jbi
>
>
>
> This is my tleap script:
>
> tleap -s -f /usr/local/amber14/dat/leap/cmd/leaprc.ff14SB
> loadamberparams frcmod.ionsjc_tip3p
> loadamberparams frcmod.phos
> loadamberprep ADP.prep
> loadamberparams frcmod.magnesium
> loadamberprep magnesium.prep
> pdb = loadpdb test.pdb
> alignaxes pdb
> center pdb
> solvateBOX pdb TIP3PBOX 12.0
> charge pdb
> addions pdb Na+ 0
> saveamberparm pdb prova.prmtop prova.rst7
>
>
> and I have the following errors:
>
> Could not find bond parameter for: O - MG Could not find bond parameter
> for: O2 - MG Could not find bond parameter for: O2 - MG Could not find bond
> parameter for: MG - O3 Could not find bond parameter for: MG - O3 Could not
> find bond parameter for: MG - O3 Building angle parameters.
> Could not find angle parameter: O - MG - O3 Could not find angle
> parameter: O - MG - O2 Could not find angle parameter: O - MG - O2 Could
> not find angle parameter: O - MG - O3 Could not find angle parameter: O -
> MG - O3 Could not find angle parameter: C - O - MG Could not find angle
> parameter: O2 - MG - O3 Could not find angle parameter: O2 - MG - O3 Could
> not find angle parameter: O2 - MG - O3 Could not find angle parameter: O2 -
> MG - O3 Could not find angle parameter: O2 - MG - O2 Could not find angle
> parameter: O2 - MG - O3 Could not find angle parameter: O2 - MG - O3 Could
> not find angle parameter: CO - O2 - MG Could not find angle parameter: CO -
> O2 - MG Could not find angle parameter: MG - O3 - P Could not find angle
> parameter: MG - O3 - P Could not find angle parameter: MG - O3 - P Could
> not find angle parameter: O3 - MG - O3 Could not find angle parameter: O3 -
> MG - O3 Could not find angle parameter: O3 - MG - O3 Building proper
> torsion parameters.
> 1-4: angle 2311 2312 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 2310 7759 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 7759 7761 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 7759 7761 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 7762 7763 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 7760 7762 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 7760 7763 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> ** No torsion terms for O-MG-O3-P
> ** No torsion terms for O-MG-O2-CO
> ** No torsion terms for O-MG-O2-CO
> ** No torsion terms for O-MG-O3-P
> ** No torsion terms for O-MG-O3-P
> ** No torsion terms for C-O-MG-O3
> ** No torsion terms for C-O-MG-O2
> ** No torsion terms for C-O-MG-O2
> ** No torsion terms for C-O-MG-O3
> ** No torsion terms for C-O-MG-O3
> ** No torsion terms for O2-CO-O2-MG
> ** No torsion terms for O2-MG-O3-P
> ** No torsion terms for O2-MG-O3-P
> ** No torsion terms for O2-MG-O3-P
> ** No torsion terms for O2-CO-O2-MG
> ** No torsion terms for O2-MG-O3-P
> ** No torsion terms for O2-MG-O3-P
> ** No torsion terms for O2-MG-O3-P
> ** No torsion terms for CO-O2-MG-O3
> ** No torsion terms for CO-O2-MG-O2
> ** No torsion terms for CO-O2-MG-O3
> ** No torsion terms for CO-O2-MG-O3
> ** No torsion terms for CO-O2-MG-O3
> ** No torsion terms for CO-O2-MG-O2
> ** No torsion terms for CO-O2-MG-O3
> ** No torsion terms for CO-O2-MG-O3
> ** No torsion terms for 2C-CO-O2-MG
> ** No torsion terms for 2C-CO-O2-MG
> ** No torsion terms for MG-O3-P-O3
> ** No torsion terms for MG-O3-P-O3
> ** No torsion terms for MG-O3-P-OS
> ** No torsion terms for MG-O3-P-O3
> ** No torsion terms for MG-O3-P-O3
> ** No torsion terms for MG-O3-P-OS
> ** No torsion terms for MG-O3-P-O3
> ** No torsion terms for MG-O3-P-O3
> ** No torsion terms for MG-O3-P-OS
> ** No torsion terms for P-O3-MG-O3
> ** No torsion terms for P-O3-MG-O3
> ** No torsion terms for P-O3-MG-O3
> ** No torsion terms for P-O3-MG-O3
> ** No torsion terms for O3-MG-O3-P
> ** No torsion terms for O3-MG-O3-P
> Building improper torsion parameters.
> old PREP-specified impropers:
> <adp 504>: C8 C4 N9 C1*
> <adp 504>: C6 H60 N6 H61
> <adp 504>: N7 N9 C8 H80
> <adp 504>: N1 N3 C2 H2
> <adp 504>: C5 N1 C6 N6
> total 1469 improper torsions applied
> 5 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Parameter file was not saved.
>
>
> Any suggestions will be highly appreciated.
>
> Thank you so much
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Received on Wed May 10 2017 - 08:30:03 PDT
