[gmx-users] How to combine Slipid FF with amber FF?
Yorquant Wang
wangykoo at gmail.com
Mon Sep 1 15:55:41 CEST 2014
Hi,
Thank you for your reply. I have added the parameters from Slipid to
amber FF files (including: atomtypes.atp, ffbonded.itp, ffnonbonded.itp). I
also get such an error.
ERROR 1 [file ffbonded.itp, line 410]:
Not enough atomtypes (1 instead of 3)
I just patch two atomtypes.atp (one from amber and another one from Slipid)
together. Could you give me some seggestions? thanks !
2014-08-31 21:13 GMT+08:00 rajat desikan <rajatdesikan at gmail.com>:
> 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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--
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai
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