[gmx-users] gromacs error
Justin Lemkul
jalemkul at vt.edu
Mon Feb 1 14:10:59 CET 2016
On 2/1/16 1:06 AM, Mehreen Jan wrote:
> how to run gromacs for protein protein interaction having phosphorylated at SER and THR.
> error:
> residue TPO not found in residue topology database
> modification are done from the given web.
> http://www.gromacs.org/Downloads/User_contributions/Force_fields
>
>> make changes in .rtp file
> make changes in .dat file
> forcefield 43A1 is used.
>
> command:
> pdb2gmx -f protein.pdb -p protein.top -o protein.gro
> error:
> residue "TPO" not found in residue topology database
>
This means whatever either (1) you did not make the changes in the
directory/file you thought or (2) you did not choose the right force field when
prompted by pdb2gmx. Without the full screen output from pdb2gmx, it's
impossible to tell.
-Justin
> make changes in residuestypes.dat
> fallowing are the changes make in .rtp file
>
> ; [ SEP ] [ TPO ] [ PTR ] -PO4^{-2} forms
> ; [ SEPH ] [ TPOH ] [ PTRH ] -PO4H^{-1} forms
>
>
> [ SEP ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 2
> OG OA -0.36000 2
> P P 0.94000 2
> O1P OP -0.86000 2
> O2P OP -0.86000 2
> O3P OP -0.86000 2
> C C 0.380 3
> O O -0.380 3
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB OG gb_17
> OG P gb_27
> P O1P gb_23
> P O2P gb_23
> P O3P gb_23
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB OG ga_12
> CB OG P ga_25
> OG P O1P ga_13
> OG P O2P ga_13
> OG P O3P ga_13
> O1P P O2P ga_28
> O1P P O3P ga_28
> O2P P O3P ga_28
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB OG gd_17
> CA CB OG P gd_14
> CB OG P O1P gd_11
>
> [ TPO ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH1 0.00000 2
> OG1 OA -0.36000 2
> P P 0.94000 2
> O1P OP -0.86000 2
> O2P OP -0.86000 2
> O3P OP -0.86000 2
> CG2 CH3 0.00000 3
> C C 0.380 4
> O O -0.380 4
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB OG1 gb_17
> CB CG2 gb_26
> OG1 P gb_27
> P O1P gb_23
> P O2P gb_23
> P O3P gb_23
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB OG1 ga_12
> CA CB CG2 ga_14
> OG1 CB CG2 ga_14
> CB OG1 P ga_25
> OG1 P O1P ga_13
> OG1 P O2P ga_13
> OG1 P O3P ga_13
> O1P P O2P ga_28
> O1P P O3P ga_28
> O2P P O3P ga_28
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> CB OG1 CG2 CA gi_2
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB OG1 gd_17
> CA CB OG1 P gd_14
> CB OG1 P O1P gd_11
>
> [ PTR ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 1
> CG C 0.00000 1
> CD1 C -0.10000 2
> HD1 HC 0.10000 2
> CD2 C -0.10000 3
> HD2 HC 0.10000 3
> CE1 C -0.10000 4
> HE1 HC 0.10000 4
> CE2 C -0.10000 5
> HE2 HC 0.10000 5
> CZ C 0.00000 6
> OH OA -0.36000 6
> P P 0.94000 6
> O1P OP -0.86000 6
> O2P OP -0.86000 6
> O3P OP -0.86000 6
> C C 0.380 7
> O O -0.380 7
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB CG gb_26
> CG CD1 gb_15
> CG CD2 gb_15
> CD1 HD1 gb_3
> CD1 CE1 gb_15
> CD2 HD2 gb_3
> CD2 CE2 gb_15
> CE1 HE1 gb_3
> CE1 CZ gb_15
> CE2 HE2 gb_3
> CE2 CZ gb_15
> CZ OH gb_12
> OH P gb_27
> P O1P gb_23
> P O2P gb_23
> P O3P gb_23
> [ exclusions ]
> ; ai aj
> CB HD1
> CB HD2
> CB CE1
> CB CE2
> CG HE1
> CG HE2
> CG CZ
> CD1 HD2
> CD1 CE2
> CD1 OH
> HD1 CD2
> HD1 HE1
> HD1 CZ
> CD2 CE1
> CD2 OH
> HD2 HE2
> HD2 CZ
> CE1 HE2
> HE1 CE2
> HE1 OH
> HE2 OH
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB CG ga_14
> CB CG CD1 ga_26
> CB CG CD2 ga_26
> CD1 CG CD2 ga_26
> CG CD1 HD1 ga_24
> HD1 CD1 CE1 ga_24
> CG CD1 CE1 ga_26
> CG CD2 HD2 ga_24
> HD2 CD2 CE2 ga_24
> CG CD2 CE2 ga_26
> CD1 CE1 HE1 ga_24
> HE1 CE1 CZ ga_24
> CD1 CE1 CZ ga_26
> CD2 CE2 HE2 ga_24
> HE2 CE2 CZ ga_24
> CD2 CE2 CZ ga_26
> CE1 CZ CE2 ga_26
> CE1 CZ OH ga_26
> CE2 CZ OH ga_26
> CZ OH P ga_25
> OH P O1P ga_13
> OH P O2P ga_13
> OH P O3P ga_13
> O1P P O2P ga_28
> O1P P O3P ga_28
> O2P P O3P ga_28
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> CG CD1 CD2 CB gi_1
> CD2 CG CD1 CE1 gi_1
> CD1 CG CD2 CE2 gi_1
> CG CD1 CE1 CZ gi_1
> CG CD2 CE2 CZ gi_1
> CD1 CE1 CZ CE2 gi_1
> CD2 CE2 CZ CE1 gi_1
> CD1 CG CE1 HD1 gi_1
> CD2 CG CE2 HD2 gi_1
> CE1 CZ CD1 HE1 gi_1
> CE2 CZ CD2 HE2 gi_1
> CZ CE1 CE2 OH gi_1
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB CG gd_17
> CA CB CG CD1 gd_20
> CE1 CZ OH P gd_14
> CZ OH P O1P gd_11
>
> ; end
>
>
> [ SEPH ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 2
> OG OA -0.36000 2
> P P 1.23000 2
> O1P OP -0.86000 2
> O2P OP -0.86000 2
> O3P OA -0.54800 2
> H3P H 0.39800 2
> C C 0.380 3
> O O -0.380 3
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB OG gb_17
> OG P gb_27
> P O1P gb_23
> P O2P gb_23
> P O3P gb_23
> O3P H3P gb_1
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB OG ga_12
> CB OG P ga_25
> OG P O1P ga_13
> OG P O2P ga_13
> OG P O3P ga_4
> O1P P O2P ga_28
> O1P P O3P ga_13
> O2P P O3P ga_13
> P O3P H3P ga_11
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB OG gd_17
> CA CB OG P gd_14
> CB OG P O1P gd_11
> OG P O3P H3P gd_11
> [ TPOH ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH1 0.00000 2
> OG1 OA -0.36000 2
> P P 1.23000 2
> O1P OP -0.86000 2
> O2P OP -0.86000 2
> O3P OA -0.54800 2
> H3P H 0.39800 2
> CG2 CH3 0.00000 3
> C C 0.380 4
> O O -0.380 4
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB OG1 gb_17
> CB CG2 gb_26
> OG1 P gb_27
> P O1P gb_23
> P O2P gb_23
> P O3P gb_23
> O3P H3P gb_1
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB OG1 ga_12
> CA CB CG2 ga_14
> OG1 CB CG2 ga_14
> CB OG1 P ga_25
> OG1 P O1P ga_13
> OG1 P O2P ga_13
> OG1 P O3P ga_4
> O1P P O2P ga_28
> O1P P O3P ga_13
> O2P P O3P ga_13
> P O3P H3P ga_11
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> CB OG1 CG2 CA gi_2
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB OG1 gd_17
> CA CB OG1 P gd_14
> CB OG1 P O1P gd_11
> OG1 P O3P H3P gd_11
> [ PTRH ]
> [ atoms ]
> N N -0.28000 0
> H H 0.28000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 1
> CG C 0.00000 1
> CD1 C -0.10000 2
> HD1 HC 0.10000 2
> CD2 C -0.10000 3
> HD2 HC 0.10000 3
> CE1 C -0.10000 4
> HE1 HC 0.10000 4
> CE2 C -0.10000 5
> HE2 HC 0.10000 5
> CZ C 0.00000 6
> OH OA -0.36000 6
> P P 1.23000 6
> O1P OP -0.86000 6
> O2P OP -0.86000 6
> O3P OA -0.54800 6
> H3P H 0.39800 6
> C C 0.380 7
> O O -0.380 7
> [ bonds ]
> N H gb_2
> N CA gb_20
> CA C gb_26
> C O gb_4
> C +N gb_9
> CA CB gb_26
> CB CG gb_26
> CG CD1 gb_15
> CG CD2 gb_15
> CD1 HD1 gb_3
> CD1 CE1 gb_15
> CD2 HD2 gb_3
> CD2 CE2 gb_15
> CE1 HE1 gb_3
> CE1 CZ gb_15
> CE2 HE2 gb_3
> CE2 CZ gb_15
> CZ OH gb_12
> OH P gb_27
> P O1P gb_23
> P O2P gb_23
> P O3P gb_23
> O3P H3P gb_1
> [ exclusions ]
> ; ai aj
> CB HD1
> CB HD2
> CB CE1
> CB CE2
> CG HE1
> CG HE2
> CG CZ
> CD1 HD2
> CD1 CE2
> CD1 OH
> HD1 CD2
> HD1 HE1
> HD1 CZ
> CD2 CE1
> CD2 OH
> HD2 HE2
> HD2 CZ
> CE1 HE2
> HE1 CE2
> HE1 OH
> HE2 OH
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_31
> H N CA ga_17
> -C N CA ga_30
> N CA C ga_12
> CA C +N ga_18
> CA C O ga_29
> O C +N ga_32
> N CA CB ga_12
> C CA CB ga_12
> CA CB CG ga_14
> CB CG CD1 ga_26
> CB CG CD2 ga_26
> CD1 CG CD2 ga_26
> CG CD1 HD1 ga_24
> HD1 CD1 CE1 ga_24
> CG CD1 CE1 ga_26
> CG CD2 HD2 ga_24
> HD2 CD2 CE2 ga_24
> CG CD2 CE2 ga_26
> CD1 CE1 HE1 ga_24
> HE1 CE1 CZ ga_24
> CD1 CE1 CZ ga_26
> CD2 CE2 HE2 ga_24
> HE2 CE2 CZ ga_24
> CD2 CE2 CZ ga_26
> CE1 CZ CE2 ga_26
> CE1 CZ OH ga_26
> CE2 CZ OH ga_26
> CZ OH P ga_25
> OH P O1P ga_13
> OH P O2P ga_13
> OH P O3P ga_4
> O1P P O2P ga_13
> O1P P O3P ga_13
> O2P P O3P ga_28
> P O3P H3P ga_11
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> C CA +N O gi_1
> CA N C CB gi_2
> CG CD1 CD2 CB gi_1
> CD2 CG CD1 CE1 gi_1
> CD1 CG CD2 CE2 gi_1
> CG CD1 CE1 CZ gi_1
> CG CD2 CE2 CZ gi_1
> CD1 CE1 CZ CE2 gi_1
> CD2 CE2 CZ CE1 gi_1
> CD1 CG CE1 HD1 gi_1
> CD2 CG CE2 HD2 gi_1
> CE1 CZ CD1 HE1 gi_1
> CE2 CZ CD2 HE2 gi_1
> CZ CE1 CE2 OH gi_1
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_4
> -C N CA C gd_19
> N CA C +N gd_20
> N CA CB CG gd_17
> CA CB CG CD1 gd_20
> CE1 CZ OH P gd_14
> CZ OH P O1P gd_11
> OH P O3P H3P gd_11
>
> ; end insert from pamac_hsn.rtp
>
>
>
>
> --------------------------------------------
> On Mon, 1/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
> Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 1
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Received: Monday, 1 February, 2016, 9:50 AM
>
> Send gromacs.org_gmx-users mailing
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>
> Today's Topics:
>
> 1. relative binding free energy
> calculation Gromacs 5.0.5
> (Stefania Evoli)
> 2. Re: relative binding free energy
> calculation Gromacs 5.0.5
> (hannes.loeffler at stfc.ac.uk)
> 3. gmx sasa (Eric Smoll)
> 4. Re: gmx sasa (Justin Lemkul)
> 5. g_count (vgsplayer1)
> 6. Re: g_count (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 31 Jan 2016 12:59:10 +0000
> From: Stefania Evoli <stefania.evoli at kaust.edu.sa>
> To: "gmx-users at gromacs.org"
> <gmx-users at gromacs.org>
> Subject: [gmx-users] relative binding free energy
> calculation Gromacs
> 5.0.5
> Message-ID: <D2D3DFC6.41F4%stefania.evoli at kaust.edu.sa>
> Content-Type: text/plain; charset="Windows-1252"
>
> Dear users,
>
> I?m performing relative binding free energy calculation in
> Gromacs 5.0.5. In the mdp files I?m using the following
> section
>
>
> free-energy
> = yes
>
> init_lambda_state = LAMBDA
>
> fep_lambdas
> = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0
> 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
>
> vdw_lambdas
> = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65
> 0.7 0.75 0.8 0.85 0.9 0.95 1.0
>
> ;couple-moltype
> = LIG
>
> ;couple-lambda0
> = vdw-q
>
> ;couple-lambda1
> = none
>
> ;couple-intramol = no
>
> sc-alpha
> = 0.5
>
> sc-sigma
> = 0.3
>
> sc-power
> = 1.0
>
> sc-r-power
> = 6
>
> sc-coul
> = no
>
> nstdhdl
> = 100
>
> calc-lambda-neighbors = -1
>
>
> And I obtained the following values
>
>
> 0 -- 1 16.498 +-
> 0.147 16.458 +-
> 0.173 18.142 +-
> 0.465 13.644 +-
> 0.351 16.264 +-
> 0.411 16.264 +- 0.413
>
> 1 -- 2
> 7.086 +- 0.143
> 6.982 +- 0.159
> 10.223 +- 0.246
> 4.168 +- 0.299
> 6.971 +- 0.341 6.971
> +- 0.454
>
> 2 -- 3
> -1.954 +- 0.114
> -1.685 +- 0.129
> -1.043 +- 0.574
> -3.884 +- 0.392
> -1.883 +- 0.356
> -1.883 +- 0.356
>
> 3 -- 4
> -13.604 +- 0.139
> -13.271 +- 0.145 -10.960
> +- 0.574 -18.048 +-
> 0.234 -14.286 +- 0.601
> -13.222 +- 0.167
>
> 4 -- 5
> 0.089 +- 0.003
> 0.093 +- 0.003
> 0.079 +- 0.005 0.099
> +- 0.003 0.091 +-
> 0.003 0.085 +- 0.000
>
> 5 -- 6
> 0.078 +- 0.004
> 0.079 +- 0.004
> 0.094 +- 0.003 0.062
> +- 0.008 0.087 +-
> 0.003 0.080 +- 0.000
>
> 6 -- 7
> 0.141 +- 0.008
> 0.130 +- 0.011
> 0.110 +- 0.017 0.170
> +- 0.001 0.170 +-
> 0.001 0.143 +- 0.001
>
> 7 -- 8
> 0.123 +- 0.005
> 0.131 +- 0.006
> 0.155 +- 0.001 0.096
> +- 0.011 0.154 +-
> 0.001 0.121 +- 0.001
>
> 8 -- 9
> 0.063 +- 0.005
> 0.063 +- 0.006
> 0.071 +- 0.011 0.056
> +- 0.001 0.056 +-
> 0.001 0.095 +- 0.001
>
> 9 -- 10
> 0.012 +- 0.004 0.002
> +- 0.005 0.028 +-
> 0.001 -0.004 +-
> 0.008 0.028 +- 0.001
> 0.065 +- 0.001
>
> 10 -- 11 0.019
> +- 0.008 0.030 +-
> 0.011 -0.036 +-
> 0.009 0.084 +- 0.011
> 0.007 +- 0.007
> 0.027 +- 0.001
>
> 11 -- 12 0.016
> +- 0.006 0.013 +-
> 0.007 0.019 +- 0.008
> 0.008 +- 0.009
> 0.018 +- 0.006
> -0.004 +- 0.000
>
> 12 -- 13 0.012
> +- 0.007 0.015 +-
> 0.008 -0.004 +-
> 0.010 0.028 +- 0.009
> 0.012 +- 0.007
> -0.018 +- 0.000
>
> 13 -- 14 -0.011
> +- 0.008 -0.010 +-
> 0.009 0.015 +- 0.011
> -0.034 +- 0.010
> -0.011 +- 0.008
> -0.034 +- 0.000
>
> 14 -- 15 -0.049
> +- 0.006 -0.049 +-
> 0.007 -0.055 +-
> 0.014 -0.044 +-
> 0.001 -0.044 +-
> 0.001 -0.054 +- 0.000
>
> 15 -- 16 -0.085
> +- 0.003 -0.086 +-
> 0.004 -0.065 +-
> 0.001 -0.104 +-
> 0.005 -0.066 +-
> 0.001 -0.078 +- 0.001
>
> 16 -- 17 -0.116
> +- 0.009 -0.116 +-
> 0.010 -0.132 +-
> 0.006 -0.100 +-
> 0.016 -0.129 +-
> 0.006 -0.109 +- 0.001
>
> 17 -- 18 -0.150
> +- 0.009 -0.145 +-
> 0.010 -0.129 +-
> 0.018 -0.159 +-
> 0.001 -0.159 +-
> 0.001 -0.151 +- 0.001
>
> 18 -- 19 -0.218
> +- 0.005 -0.220 +-
> 0.005 -0.219 +-
> 0.002 -0.218 +-
> 0.008 -0.219 +-
> 0.002 -0.211 +- 0.001
>
> It is clear the instability of the first four lambda values.
> Can someone suggest me a way to avoid it? I?m trying to use
> different sc-alpha, sc-power and sc-r-power. Any
> suggestion?
>
> Thank you,
> Stefania
>
> ?
> Dr. Stefania Evoli
> Post-Doctoral Fellow
> King Abdullah University of Science and Technology
> Catalysis center - Bldg. 3, 4th floor, 4231?WS18
> Thuwal, Kingdom of Saudi Arabia
> stefania.evoli at kaust.edu.sa
>
>
>
> ________________________________
>
> This message and its contents including attachments are
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>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 31 Jan 2016 15:13:36 +0000
> From: <hannes.loeffler at stfc.ac.uk>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] relative binding free energy
> calculation
> Gromacs 5.0.5
> Message-ID:
> <5FF52965BBB9CB46930C7E5D323EC021E6C99BB1 at EXCHMBX01.fed.cclrc.ac.uk>
> Content-Type: text/plain; charset="Windows-1252"
>
> What do you mean by "instability"? You also don't
> quite say what these values mean but I guess they are the
> estimates of the free energy per each window as computed by
> different methods(?). These values come obviously from
> the (linear) electrostatic transformation so playing with
> softcore parameters won't make any difference.
>
> If you are concerned by their magnitudes you can always
> introduce additional lambda points. BTW, you may want
> to keep the mass-lambdas at their initial values (see
> mailing list archive for details).
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [gromacs.org_gmx-users-bounces at maillist.sys.kth.se]
> on behalf of Stefania Evoli [stefania.evoli at kaust.edu.sa]
> Sent: 31 January 2016 12:59
> To: gmx-users at gromacs.org
> Subject: [gmx-users] relative binding free energy
> calculation Gromacs 5.0.5
>
> Dear users,
>
> I?m performing relative binding free energy calculation in
> Gromacs 5.0.5. In the mdp files I?m using the following
> section
>
>
> free-energy
> = yes
>
> init_lambda_state = LAMBDA
>
> fep_lambdas
> = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0
> 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
>
> vdw_lambdas
> = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65
> 0.7 0.75 0.8 0.85 0.9 0.95 1.0
>
> ;couple-moltype
> = LIG
>
> ;couple-lambda0
> = vdw-q
>
> ;couple-lambda1
> = none
>
> ;couple-intramol = no
>
> sc-alpha
> = 0.5
>
> sc-sigma
> = 0.3
>
> sc-power
> = 1.0
>
> sc-r-power
> = 6
>
> sc-coul
> = no
>
> nstdhdl
> = 100
>
> calc-lambda-neighbors = -1
>
>
> And I obtained the following values
>
>
> 0 -- 1 16.498 +-
> 0.147 16.458 +-
> 0.173 18.142 +-
> 0.465 13.644 +-
> 0.351 16.264 +-
> 0.411 16.264 +- 0.413
>
> 1 -- 2
> 7.086 +- 0.143
> 6.982 +- 0.159
> 10.223 +- 0.246
> 4.168 +- 0.299
> 6.971 +- 0.341 6.971
> +- 0.454
>
> 2 -- 3
> -1.954 +- 0.114
> -1.685 +- 0.129
> -1.043 +- 0.574
> -3.884 +- 0.392
> -1.883 +- 0.356
> -1.883 +- 0.356
>
> 3 -- 4
> -13.604 +- 0.139
> -13.271 +- 0.145 -10.960
> +- 0.574 -18.048 +-
> 0.234 -14.286 +- 0.601
> -13.222 +- 0.167
>
> 4 -- 5
> 0.089 +- 0.003
> 0.093 +- 0.003
> 0.079 +- 0.005 0.099
> +- 0.003 0.091 +-
> 0.003 0.085 +- 0.000
>
> 5 -- 6
> 0.078 +- 0.004
> 0.079 +- 0.004
> 0.094 +- 0.003 0.062
> +- 0.008 0.087 +-
> 0.003 0.080 +- 0.000
>
> 6 -- 7
> 0.141 +- 0.008
> 0.130 +- 0.011
> 0.110 +- 0.017 0.170
> +- 0.001 0.170 +-
> 0.001 0.143 +- 0.001
>
> 7 -- 8
> 0.123 +- 0.005
> 0.131 +- 0.006
> 0.155 +- 0.001 0.096
> +- 0.011 0.154 +-
> 0.001 0.121 +- 0.001
>
> 8 -- 9
> 0.063 +- 0.005
> 0.063 +- 0.006
> 0.071 +- 0.011 0.056
> +- 0.001 0.056 +-
> 0.001 0.095 +- 0.001
>
> 9 -- 10
> 0.012 +- 0.004 0.002
> +- 0.005 0.028 +-
> 0.001 -0.004 +-
> 0.008 0.028 +- 0.001
> 0.065 +- 0.001
>
> 10 -- 11 0.019
> +- 0.008 0.030 +-
> 0.011 -0.036 +-
> 0.009 0.084 +- 0.011
> 0.007 +- 0.007
> 0.027 +- 0.001
>
> 11 -- 12 0.016
> +- 0.006 0.013 +-
> 0.007 0.019 +- 0.008
> 0.008 +- 0.009
> 0.018 +- 0.006
> -0.004 +- 0.000
>
> 12 -- 13 0.012
> +- 0.007 0.015 +-
> 0.008 -0.004 +-
> 0.010 0.028 +- 0.009
> 0.012 +- 0.007
> -0.018 +- 0.000
>
> 13 -- 14 -0.011
> +- 0.008 -0.010 +-
> 0.009 0.015 +- 0.011
> -0.034 +- 0.010
> -0.011 +- 0.008
> -0.034 +- 0.000
>
> 14 -- 15 -0.049
> +- 0.006 -0.049 +-
> 0.007 -0.055 +-
> 0.014 -0.044 +-
> 0.001 -0.044 +-
> 0.001 -0.054 +- 0.000
>
> 15 -- 16 -0.085
> +- 0.003 -0.086 +-
> 0.004 -0.065 +-
> 0.001 -0.104 +-
> 0.005 -0.066 +-
> 0.001 -0.078 +- 0.001
>
> 16 -- 17 -0.116
> +- 0.009 -0.116 +-
> 0.010 -0.132 +-
> 0.006 -0.100 +-
> 0.016 -0.129 +-
> 0.006 -0.109 +- 0.001
>
> 17 -- 18 -0.150
> +- 0.009 -0.145 +-
> 0.010 -0.129 +-
> 0.018 -0.159 +-
> 0.001 -0.159 +-
> 0.001 -0.151 +- 0.001
>
> 18 -- 19 -0.218
> +- 0.005 -0.220 +-
> 0.005 -0.219 +-
> 0.002 -0.218 +-
> 0.008 -0.219 +-
> 0.002 -0.211 +- 0.001
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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