[gmx-users] How to combine Slipid FF with amber FF?
Justin Lemkul
jalemkul at vt.edu
Mon Sep 1 19:24:55 CEST 2014
On 9/1/14, 9:55 AM, Yorquant Wang wrote:
> 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 !
>
The error has nothing to do with atomtypes.atp, it's coming from ffbonded.itp
(line 410). It looks like you're adding a directive incorrectly. Atom type
parameters go in ffnonbonded.itp; the line above indicates that grompp is
looking for 3 atom types in sequence, so it wants an angle, but finds 1 atom type.
-Justin
>
> 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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>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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