Yes I did it but it return the following error:
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: MG - O3
Building angle parameters.
Could not find angle parameter: MG - O3 - P
Building proper torsion parameters.
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-O3
** No torsion terms for MG-O3-P-OS
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.
>
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
source leaprc.gaff
pdb = loadpdb test.pdb
alignaxes pdb
center pdb
solvateBOX pdb TIP3PBOX 12.0
charge pdb
addions pdb Na+ 0
saveamberparm pdb test.prmtop test.rst7
2017-05-11 6:48 GMT+02:00 Elvis Martis <elvis.martis.bcp.edu.in>:
> 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
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed May 10 2017 - 23:00:02 PDT
