[gmx-users] How to combine Slipid FF with amber FF?
rajat desikan
rajatdesikan at gmail.com
Sun Aug 31 15:13:34 CEST 2014
Hi,
I assumed that you had gone through the forcefield.ff files on Slipids
webpage. You need to include the following section at the end in your
ffnonbonded.itp (some of the spaces may be missing below). I suggest
modifying a local copy of your desired Amber ff.
; SLIPIDS STARTS HERE
HAL1 1 1.008000 0.09 A 0.235197261589 0.092048
HL 1 1.008000 0.25 A 0.12472582054 0.192464
HEL1 1 1.008000 0.15 A 0.2 0.10 ; New
CL 6 12.01100 0.62 A 0.356359487256 0.29288
CTL1 6 12.01100 0.14 A 0.405358916754 0.08368
CTL3 6 12.0111 -0.081 A 0.35000 0.3400 ; New
CTL2 6 12.0011 0.05 A 0.35800 0.22800 ; New
HAL3 1 1.00800 0.09 A 0.22000 0.09500 ; New
HAL2 1 1.00800 0.09 A 0.24000 0.1120 ; New
CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472
CEL1 6 12.01100 -0.15 A 0.35 0.22 ; New
CET1 6 12.01100 -0.15 A 0.35 0.22 ; New, for trans double-bond
OBL 8 15.999400 -0.52 A 0.302905564168 0.50208
OCL 8 15.999400 -0.76 A 0.302905564168 0.50208
O2L 8 15.999400 -0.78 A 0.302905564168 0.50208
OSL 8 15.999400 -0.49 A 0.293996576986 0.4184 ; Different to C27
OSLP 8 15.999400 -0.57 A 0.293996576986 0.4184 ; Not in C27
NTL 7 14.00700 -0.60 A 0.329632525712 0.8368
PL 15 30.974000 1.50 A 0.3830864488 2.44764
HOL 1 1.008000 0.43 A 0.0400013524445 0.192464
OHL 8 15.999400 -0.66 A 0.315378146222 0.6363864
NH3L 7 14.00700 -0.30 A 0.329632525712 0.8368
HCL 1 1.008000 0.33 A 0.0400013524445 0.192464
CCL 6 12.01100 0.34 A 0.356359487256 0.29288
HBL 1 1.008000 0.10 A 0.235197261589 0.092048
NH1 7 14.00700 -0.47 A 0.329632525712 0.8368
H11 1 1.008000 0.31 A 0.0400013524445 0.192464
[ pairtypes ]
; 1-4 interactions
; i j func sigma1-4 epsilon1-4
CTL1 CTL1 1 0.338541512893 0.04184
CTL1 CTL2 1 0.338541512893 0.04184
CTL1 CTL3 1 0.338541512893 0.04184
CTL1 CTL5 1 0.338541512893 0.04184
CTL1 OBL 1 0.293996576986 0.144938011577
CTL1 HAL1 1 0.286869387241 0.06205874894
CTL1 HAL2 1 0.288651184678 0.0700117110204
CTL1 HAL3 1 0.288651184678 0.0648182492821
CTL1 HL 1 0.231633666716 0.0897368027066
CTL1 HEL1 1 0.280633096214 0.0736669217492
CTL1 CEL1 1 0.355468588538 0.109105371453
CTL1 CET1 1 0.355468588538 0.109105371453
CTL1 OSL 1 0.316269044940 0.132309697301
CTL1 OSLP 1 0.316269044940 0.132309697301
CTL1 NTL 1 0.334087019303 0.187114168357
CTL1 PL 1 0.360813980846 0.320014464673
CTL1 HOL 1 0.189271432669 0.0897368027066
CTL1 OHL 1 0.326959829558 0.163176
;
CTL2 CTL2 1 0.321 0.08184 ; New
CTL2 HAL2 1 0.268651184678 0.0200117110204 ; New
CTL2 CTL3 1 0.325 0.10184 ; New
CTL3 HAL2 1 0.278651184678 0.0200117110204 ; New
CTL2 CTL5 1 0.338541512893 0.04184
CTL2 OBL 1 0.293996576986 0.144938011577
CTL2 HAL1 1 0.286869387241 0.06205874894
CTL2 HAL3 1 0.288651184678 0.0648182492821
CTL2 HL 1 0.231633666716 0.0897368027066
CTL2 HEL1 1 0.280633096214 0.0736669217492
CTL2 CL 1 0.347450500074 0.110698234855
CTL2 CEL1 1 0.355468588538 0.109105371453
CTL2 CET1 1 0.355468588538 0.109105371453
CTL2 OCL 1 0.320723538531 0.144938011577
CTL2 O2L 1 0.320723538531 0.144938011577
CTL2 OSL 1 0.316269044940 0.132309697301
CTL2 OSLP 1 0.316269044940 0.132309697301
CTL2 NTL 1 0.334087019303 0.187114168357
CTL2 PL 1 0.360813980846 0.320014464673
CTL2 HOL 1 0.189271432669 0.0897368027066
CTL2 OHL 1 0.326959829558 0.163176
CTL2 HCL 1 0.189271432669 0.0897368027066
CTL2 NH3L 1 0.334087019303 0.187114168357
CTL2 OCL 1 0.320723538531 0.144938011577
CTL2 HCL 1 0.189271432669 0.0897368027066
;
CTL3 CTL3 1 0.338541512893 0.04184
CTL3 CTL5 1 0.338541512893 0.04184
CTL3 OBL 1 0.293996576986 0.144938011577
CTL3 HL 1 0.231633666716 0.0897368027066
CTL3 HEL1 1 0.280633096214 0.0736669217492
CTL3 CL 1 0.347450500074 0.110698234855
CTL3 CEL1 1 0.355468588538 0.109105371453
CTL3 CET1 1 0.355468588538 0.109105371453
CTL3 O2L 1 0.320723538531 0.144938011577
CTL3 OSL 1 0.316269044940 0.132309697301
CTL3 OSLP 1 0.316269044940 0.132309697301
CTL3 NTL 1 0.334087019303 0.187114168357
CTL3 PL 1 0.360813980846 0.320014464673
CTL3 HOL 1 0.189271432669 0.0897368027066
CTL3 OHL 1 0.326959829558 0.163176
;
CTL5 CTL5 1 0.338541512893 0.04184
CTL5 OBL 1 0.293996576986 0.144938011577
CTL5 HAL1 1 0.286869387241 0.06205874894
CTL5 HAL2 1 0.288651184678 0.0700117110204
CTL5 HAL3 1 0.288651184678 0.0648182492821
CTL5 HL 1 0.231633666716 0.0897368027066
CTL5 HEL1 1 0.280633096214 0.0736669217492
CTL5 CL 1 0.347450500074 0.110698234855
CTL5 CEL1 1 0.355468588538 0.109105371453
CTL5 CET1 1 0.355468588538 0.109105371453
CTL5 OCL 1 0.320723538531 0.144938011577
CTL5 O2L 1 0.320723538531 0.144938011577
CTL5 OSL 1 0.316269044940 0.132309697301
CTL5 OSLP 1 0.316269044940 0.132309697301
CTL5 NTL 1 0.334087019303 0.187114168357
CTL5 PL 1 0.360813980846 0.320014464673
;
OBL OBL 1 0.249451641079 0.50208
OBL HAL1 1 0.242324451334 0.214977812437
OBL HAL2 1 0.24410624877 0.242527681224
OBL HAL3 1 0.24410624877 0.224537002029
OBL HL 1 0.18708873081 0.310857403193
OBL HEL1 1 0.236088160307 0.255189702614
OBL CL 1 0.302905564167 0.383469934154
OBL CEL1 1 0.310923652631 0.377952093472
OBL CET1 1 0.310923652631 0.377952093472
OBL OCL 1 0.276178602624 0.50208
OBL O2L 1 0.276178602624 0.50208
OBL OSL 1 0.271724109033 0.45833423612
OBL OSLP 1 0.271724109033 0.45833423612
OBL NTL 1 0.289542083396 0.648182492821
OBL PL 1 0.316269044939 1.10856262394
Similarly, you have to make changes in the ffbonded.itp as well (add
bond, angle, proper and improper dihedral definitions). Go through the
Slipid forcefield.ff files carefully.
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