| 查看: 136 | 回复: 0 | |||
| 当前主题已经存档。 | |||
[交流]
conversion of torsional parameters to AMBER format
|
|||
|
大家好，请教一个关于amber力场中计算二面角能量的问题： 在gaff中（一个与AMBER力场自洽的力场，可以看作是amber力场），比如c3-c3-c3-c3 的参数形式为：----dihe idiv Vn/2 phase pn c3-c3-c3-c3 1 0.18 0.0 -3. Junmei et al, 1999 c3-c3-c3-c3 1 0.25 180.0 -2. Junmei et al, 1999 c3-c3-c3-c3 1 0.20 180.0 1. Junmei et al, 1999 ----计算torsional energy的公式ET=Vn/(2*idiv)*(1+cos(|pn|*phi-phase)1。 我的问题是，对于上述二面角参数计算扭转能是否是一下的形式呢：E(torsion for CT-CT-CT-CT ) = ( pk1*(1 + Cos[pn1*phi - phase1]) + pk2*(1 + Cos[pn2*phi - phase2]) + pk3*(1 + Cos[pn3*phi - phase3]) ) where pk1 = 0.20; pk2 = 0.25; pk3 = 0.18; phase1 = Pi; phase2 = Pi; phase3 = 0; pn1 = 1; pn2 = 2; pn3 = 3 ? 2。我想把一篇文献中的参数转化成amber的格式，但是按照上述公式的计算总不能与MacroModel提供的一个测试给出的能量相一致 DIHEDRAL ANGLES AND TORSIONAL ENERGIES 137 Proper Torsion interactions present -------------------------------------- Atom Numbers Force Consts Angle Energy V1/2 V2/2 V3/2 kJ/mol Select Alts Comments FF Line 1 31 36 37 -0.354 0.521 0.475 17.6 3.656 P3 0 HOPT 484 1 31 36 39 1.114 0.143 0.008 136.4 1.909 P3 0 XOPT 482 1 31 36 38 -0.354 0.521 0.475 -99.2 8.874 P3 0 HOPT -----请教大家该怎么转换上述V1/2, V2/2, V3/2的参数为amber力场中的形式能得到上述对应的能量呢？?非常感谢！－－－Jeffrey -------------------更详细的描述： Dear everyone, I'd like to perform MD simulation of system with a cofactor, AdoMet, which contains a sulfonium group. I don't know whether GAFF now provides parameters of such a group. Someone suggested me to use the parameters prepared in Biochem2002v41p7636 (supporting material, see the attachment) for this group. I first used the antechamber to prepare the prep and frcmod file, then modified the bond, angle and dihedral parameters to the ones of Biochem2002v41p7636 in frcmod file. For bond and angle parameters, it is ok to set a consistent form as that in AMBER ff (gaff.dat). As in gaff.dat, the torsional parameters are given as the following forms, ---- c3-c3-c3-c3 1 0.18 0.0 -3. Junmei et al, 1999 c3-c3-c3-c3 1 0.25 180.0 -2. Junmei et al, 1999 c3-c3-c3-c3 1 0.20 180.0 1. Junmei et al, 1999 ---- while the new parameters for sulfonium group are given in the forms as, ----- Torsional Interaction (Kcal/mol) V1/2 V2/2 V3/2 SP – CT – CT – CT -1.6814 1.0698 -0.0001 SP – CT – CT – H1 0.9529 1.1047 0.0695 ----- So I have to find a way to convert the parameters to the same form in gaff.dat. Taking the c3-c3-c3-c3 as an example, should the total torsional energy for this dihedral be E(torsion for CT-CT-CT-CT ) = ( pk1*(1 + Cos[pn1*phi - phase1]) + pk2*(1 + Cos[pn2*phi - phase2]) + pk3*(1 + Cos[pn3*phi - phase3]) ) where pk1 = 0.20; pk2 = 0.25; pk3 = 0.18; phase1 = Pi; phase2 = Pi; phase3 = 0; pn1 = 1; pn2 = 2; pn3 = 3 ? The author of Biochem2002v41p7636 sent me a testing run of AdoMet in MacroModel in which energy values and torsional parameters for each dihedral term were listed. I am trying to use the above expression to assign the pn and phase values for the sulfonium group by using V1/2, V2/2, V3/2 parameters provided in Biochem2002v41p7636 and then calculate the torsional energy to compare with the results of the testing run. I tried every method I could think of to set the pn and phase values to obtain a correct form of the torsional energy expression, but failed to. Though replies from AMBER mailing list give me much better understanding to this question, I still can't find a way to convert these parameters correctly. So I have to request your great help on this question. Any suggestion is greatly appreciated. Thanks so much for the time. Have a nice day. Best. ---- Jeffrey 1. Parameters in the supporting material of Biochem2002v41p7636 --------------- Part A. AMBER* Parameters for Sulfonium Sulfur (atom type SP) Stretching Interactions Bond Length Force Constant Bond Moment SP – CT 1.7798 345.2802 -2.4723 SP – H1 1.3546 295.8220 -1.5174 CT – H1 1.0767 398.8672 -0.8033 Bending Interactions Angle (° ) Force Constant (Kcal/mol) CT – SP – CT 100.5458 289.2187 CT – SP – H1 100.8671 137.5550 H1 - SP - H1 94.8664 59.7155 SP – CT – CT 110.2762 96.0581 SP – CT – CU 99.0741 140.8276 SP – CT – H1 104.4390 33.0448 Torsional Interaction (Kcal/mol) V1/2 V2/2 V3/2 SP – CT – CT – CT -1.6814 1.0698 -0.0001 SP – CT – CT – H1 0.9529 1.1047 0.0695 SP – CT – CT – O3 3.5661 0.5502 -0.0208 SP – CT – CU – O0 2.6315 7.8116 0.2180 CT – SP – CT – CT 1.1139 0.1433 0.0082 CT – SP – CT – CU -3.2131 -0.5355 -0.2743 CT – SP – CT – H1 -0.3536 0.5214 0.4750 H1 – SP – CT – CT 0.0340 -0.2867 0.2474 H1 – SP – CT – CU 0.0340 -0.2867 0.2474 H1 – SP – CT – H1 0.2150 -0.2420 0.0732 ----------------- 2. part of the testing run of AdoMet in MacroModel: ------- DIHEDRAL ANGLES AND TORSIONAL ENERGIES 137 Proper Torsion interactions present -------------------------------------- Atom Numbers Force Consts Angle Energy V1/2 V2/2 V3/2 kJ/mol Select Alts Comments FF Line 1 31 36 37 -0.354 0.521 0.475 17.6 3.656 P3 0 HOPT 484 1 31 36 39 1.114 0.143 0.008 136.4 1.909 P3 0 XOPT 482 1 31 36 38 -0.354 0.521 0.475 -99.2 8.874 P3 0 HOPT 484 1 31 32 33 -0.354 0.521 0.475 173.9 3.102 P3 0 HOPT 484 1 31 32 34 -0.354 0.521 0.475 -67.1 4.747 P3 0 HOPT 484 1 31 32 35 -0.354 0.521 0.475 51.6 3.431 P3 0 HOPT 484 1 2 3 8 0.767 -0.110 0.300 160.6 1.594 A1 0 C-C-O-C, HS (Me-O-Et,AA)(CU) 619 1 2 4 5 0.000 0.000 0.144 82.5 0.372 O1 0 -C-C- 699 1 2 4 6 0.000 0.000 0.144 -161.3 0.267 O1 0 -C-C- 699 1 2 4 22 0.000 0.000 0.144 -45.2 0.171 O1 0 -C-C- 699 2 1 31 36 1.114 0.143 0.008 -166.6 0.198 P3 0 XOPT 482 2 1 31 32 1.114 0.143 0.008 88.9 5.978 P3 0 XOPT 482 2 3 8 6 0.767 -0.110 0.300 -15.4 9.281 A1 0 C-C-O-C, HS (Me-O-Et,AA)(CU) 619 2 3 8 9 0.000 0.000 0.383 -137.4 2.588 O1 0 -C-O-X (X.NE.H) 734 2 3 8 26 0.000 0.000 0.383 102.6 2.590 O1 0 -C-O-X (X.NE.H) 734 2 4 5 23 0.100 0.000 0.110 -83.4 0.770 M1 0 H-O-C-X, WCS (CU) 635 2 4 6 7 0.000 0.000 0.144 -87.9 0.538 O1 0 -C-C- 699 2 4 6 8 0.000 0.000 0.144 29.0 0.635 O1 0 -C-C- 699 2 4 6 24 0.000 0.000 0.144 151.8 0.547 O1 0 -C-C- 699 3 2 1 31 3.566 0.550 -0.021 -69.1 24.428 P3 0 XOPT ....... --------- 非常感谢！ [ Last edited by lei0736 on 2009-11-25 at 13:02 ] |
回复此楼» 猜你喜欢
全日制（定向）博士
已经有5人回复
-
假如你的研究生提出不合理要求
已经有10人回复
-
萌生出自己或许不适合搞科研的想法，现在跑or等等看？
已经有4人回复
-
Materials Today Chemistry审稿周期
已经有4人回复
-
参与限项
已经有3人回复
-
实验室接单子
已经有4人回复
-
对氯苯硼酸纯化
已经有3人回复
-
求助:我三月中下旬出站，青基依托单位怎么办？
已经有12人回复
-
所感
已经有4人回复
-
要不要辞职读博？
已经有7人回复