Hi,
did you try loading gaff force field in leap and repeat what you did?
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
Skype. adrian_elvis12
-----Original Message-----
From: Tommaso Biagini [mailto:tommasobiagini.gmail.com]
Sent: Thursday, May 11, 2017 9:47 AM
To: kungking Hanpaibool <kunkungking.hotmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MG angle parameter
how can i build the correct or download adp mg2+ prep file?
Il 10 mag 2017 5:25 PM, "kungking Hanpaibool" <kunkungking.hotmail.com> ha
scritto:
> 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
> > Skype. adrian_elvis12
> >
> >
> >
> >
> > -----Original Message-----
> > From: Tommaso Biagini [mailto:tommasobiagini.gmail.com
> <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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> >
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Received on Wed May 10 2017 - 22:00:03 PDT
