[gmx-users] ADP topology parameter
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Mon Mar 15 15:37:01 CET 2004
Hi Zhiguo
You don't say what you use for input - remember the server cannot correct
for mistakes in either PDB file or 2D structure input. I.e. it works with
the GIGO principle (Garbage-In-Garbage-Out). In my experience, 9 out of 10
times when things go wrong it is because of inconsistencies in the user
input....
Daan
On Sun, 14 Mar 2004, Zhiguo Liu wrote:
> Dear gmx-users £¬
> I used dundee server to generate the topology file of ADP. The ADP topol structure turned to be extremely distorted after I minimized for about 2000 steps in water and mdrun ended with message "converged to machine precision". Then I checked the ADP's itp file. The atom types of "O" binded to "P" (atom 1,3,4, and 7,8) seem confusing. I wonder if the atom types here are right? If not, what kind of atom type should be give to the "O" in "P=O" , "P-O^"("O" with -1 charge), and "P-O-C" respectively?
> Here is what atom type I think should be changed to: 1(OM),3(OM),4(O),7(OM),8(O),10(CS2). Could anyone give some advice?
>
>
>
> ADP.itp file:
>
> ######################################################
> [ moleculetype ]
> ;name nrexcl
> ADP 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge
> 1 OA 1 ADP O2B 1 -1.077
> 2 P 1 ADP PB 1 1.547
> 3 OA 1 ADP O3B 1 -1.017
> 4 OM 1 ADP O1B 1 -1.008
> 5 OS 1 ADP O3A 2 -0.658
> 6 P 1 ADP PA 2 1.545
> 7 OM 1 ADP O1A 2 -0.945
> 8 OM 1 ADP O2A 2 -0.877
> 9 OS 1 ADP O5* 2 -0.641
> 10 CH2 1 ADP C5* 3 0.302
> 11 CS1 1 ADP C4* 3 0.207
> 12 OS 1 ADP O4* 3 -0.579
> 13 CH1 1 ADP C3* 4 0.455
> 14 OA 1 ADP O3* 4 -0.857
> 15 HO 1 ADP HAA 4 0.501
> 16 CH1 1 ADP C2* 5 0.227
> 17 OA 1 ADP O2* 5 -0.806
> 18 HO 1 ADP HAB 5 0.466
> 19 CS1 1 ADP C1* 6 0.633
> 20 NR5* 1 ADP N9 6 -0.521
> 21 CR51 1 ADP C8 6 0.617
> 22 NR5 1 ADP N7 6 -0.650
> 23 CB 1 ADP C5 6 -0.140
> 24 CB 1 ADP C4 7 0.690
> 25 NR6 1 ADP N3 7 -0.890
> 26 CR61 1 ADP C2 7 0.672
> 27 NR6 1 ADP N1 7 -0.934
> 28 CB 1 ADP C6 8 0.924
> 29 NT 1 ADP N6 8 -1.033
> 30 H 1 ADP HAD 8 0.411
> 31 H 1 ADP HAC 8 0.436
> [ bonds ]
> ;ai aj fu c0 c1
> 1 2 1 0.161 251040.0 0.161 251040.0 ; O2B PB
> 2 3 1 0.161 251040.0 0.161 251040.0 ; PB O3B
> 2 4 1 0.148 376560.0 0.148 376560.0 ; PB O1B
> 2 5 1 0.161 251040.0 0.161 251040.0 ; PB O3A
> 5 6 1 0.161 251040.0 0.161 251040.0 ; O3A PA
> 6 7 1 0.148 376560.0 0.148 376560.0 ; PA O1A
> 6 8 1 0.148 376560.0 0.148 376560.0 ; PA O2A
> 6 9 1 0.161 251040.0 0.161 251040.0 ; PA O5*
> 9 10 1 0.143 251040.0 0.143 251040.0 ; O5* C5*
> 10 11 1 0.153 251040.0 0.153 251040.0 ; C5* C4*
> 11 12 1 0.144 251040.0 0.144 251040.0 ; C4* O4*
> 11 13 1 0.153 334720.0 0.153 334720.0 ; C4* C3*
> 12 19 1 0.144 251040.0 0.144 251040.0 ; O4* C1*
> 13 14 1 0.143 334720.0 0.143 334720.0 ; C3* O3*
> 13 16 1 0.153 334720.0 0.153 334720.0 ; C3* C2*
> 14 15 1 0.100 313800.0 0.100 313800.0 ; O3* HAA
> 16 17 1 0.143 334720.0 0.143 334720.0 ; C2* O2*
> 16 19 1 0.153 334720.0 0.153 334720.0 ; C2* C1*
> 17 18 1 0.100 313800.0 0.100 313800.0 ; O2* HAB
> 19 20 1 0.148 251040.0 0.148 251040.0 ; C1* N9
> 20 21 1 0.133 418400.0 0.133 418400.0 ; N9 C8
> 20 24 1 0.133 418400.0 0.133 418400.0 ; N9 C4
> 21 22 1 0.133 418400.0 0.133 418400.0 ; C8 N7
> 22 23 1 0.133 418400.0 0.133 418400.0 ; N7 C5
> 23 24 1 0.139 418400.0 0.139 418400.0 ; C5 C4
> 23 28 1 0.139 418400.0 0.139 418400.0 ; C5 C6
> 24 25 1 0.134 418400.0 0.134 418400.0 ; C4 N3
> 25 26 1 0.132 418400.0 0.132 418400.0 ; N3 C2
> 26 27 1 0.132 418400.0 0.132 418400.0 ; C2 N1
> 27 28 1 0.134 418400.0 0.134 418400.0 ; N1 C6
> 28 29 1 0.133 376560.0 0.133 376560.0 ; C6 N6
> 29 30 1 0.100 374468.0 0.100 374468.0 ; N6 HAD
> 29 31 1 0.100 374468.0 0.100 374468.0 ; N6 HAC
> [ pairs ]
> ;ai aj fu c0 c1
> 1 6 1 ; O2B PA
> 2 7 1 ; PB O1A
> 2 8 1 ; PB O2A
> 2 9 1 ; PB O5*
> 3 6 1 ; O3B PA
> 4 6 1 ; O1B PA
> 5 10 1 ; O3A C5*
> 6 11 1 ; PA C4*
> 7 10 1 ; O1A C5*
> 8 10 1 ; O2A C5*
> 9 12 1 ; O5* O4*
> 9 13 1 ; O5* C3*
> 10 14 1 ; C5* O3*
> 10 16 1 ; C5* C2*
> 10 19 1 ; C5* C1*
> 11 15 1 ; C4* HAA
> 11 17 1 ; C4* O2*
> 11 20 1 ; C4* N9
> 12 14 1 ; O4* O3*
> 12 17 1 ; O4* O2*
> 12 21 1 ; O4* C8
> 12 24 1 ; O4* C4
> 13 18 1 ; C3* HAB
> 13 20 1 ; C3* N9
> 14 17 1 ; O3* O2*
> 14 19 1 ; O3* C1*
> 15 16 1 ; HAA C2*
> 16 21 1 ; C2* C8
> 16 24 1 ; C2* C4
> 17 20 1 ; O2* N9
> 18 19 1 ; HAB C1*
> 19 22 1 ; C1* N7
> 19 23 1 ; C1* C5
> 19 25 1 ; C1* N3
> 20 26 1 ; N9 C2
> 20 28 1 ; N9 C6
> 21 25 1 ; C8 N3
> 21 28 1 ; C8 C6
> 22 25 1 ; N7 N3
> 22 27 1 ; N7 N1
> 22 29 1 ; N7 N6
> 23 26 1 ; C5 C2
> 23 30 1 ; C5 HAD
> 23 31 1 ; C5 HAC
> 24 27 1 ; C4 N1
> 24 29 1 ; C4 N6
> 25 28 1 ; N3 C6
> 26 29 1 ; C2 N6
> 27 30 1 ; N1 HAD
> 27 31 1 ; N1 HAC
> [ angles ]
> ;ai aj ak fu c0 c1
> 1 2 3 1 103.0 397.5 103.0 397.5 ; O2B PB O3B
> 1 2 4 1 109.6 397.5 109.6 397.5 ; O2B PB O1B
> 3 2 4 1 109.6 397.5 109.6 397.5 ; O3B PB O1B
> 1 2 5 1 103.0 397.5 103.0 397.5 ; O2B PB O3A
> 3 2 5 1 103.0 397.5 103.0 397.5 ; O3B PB O3A
> 4 2 5 1 109.6 397.5 109.6 397.5 ; O1B PB O3A
> 2 5 6 1 120.0 397.5 120.0 397.5 ; PB O3A PA
> 5 6 7 1 109.6 397.5 109.6 397.5 ; O3A PA O1A
> 5 6 8 1 109.6 397.5 109.6 397.5 ; O3A PA O2A
> 7 6 8 1 120.0 585.8 120.0 585.8 ; O1A PA O2A
> 5 6 9 1 103.0 397.5 103.0 397.5 ; O3A PA O5*
> 7 6 9 1 109.6 397.5 109.6 397.5 ; O1A PA O5*
> 8 6 9 1 109.6 397.5 109.6 397.5 ; O2A PA O5*
> 6 9 10 1 120.0 397.5 120.0 397.5 ; PA O5* C5*
> 9 10 11 1 111.0 460.2 111.0 460.2 ; O5* C5* C4*
> 10 11 12 1 109.5 284.5 109.5 284.5 ; C5* C4* O4*
> 10 11 13 1 109.5 251.0 109.5 251.0 ; C5* C4* C3*
> 12 11 13 1 104.0 460.2 104.0 460.2 ; O4* C4* C3*
> 11 12 19 1 104.0 460.2 104.0 460.2 ; C4* O4* C1*
> 11 13 14 1 109.5 460.2 109.5 460.2 ; C4* C3* O3*
> 11 13 16 1 104.0 460.2 104.0 460.2 ; C4* C3* C2*
> 14 13 16 1 109.5 460.2 109.5 460.2 ; O3* C3* C2*
> 13 14 15 1 109.5 397.5 109.5 397.5 ; C3* O3* HAA
> 13 16 17 1 109.5 460.2 109.5 460.2 ; C3* C2* O2*
> 13 16 19 1 104.0 460.2 104.0 460.2 ; C3* C2* C1*
> 17 16 19 1 109.5 460.2 109.5 460.2 ; O2* C2* C1*
> 16 17 18 1 109.5 397.5 109.5 397.5 ; C2* O2* HAB
> 12 19 16 1 104.0 460.2 104.0 460.2 ; O4* C1* C2*
> 12 19 20 1 109.5 284.5 109.5 284.5 ; O4* C1* N9
> 16 19 20 1 109.5 284.5 109.5 284.5 ; C2* C1* N9
> 19 20 21 1 126.0 418.4 126.0 418.4 ; C1* N9 C8
> 19 20 24 1 126.0 418.4 126.0 418.4 ; C1* N9 C4
> 21 20 24 1 108.0 418.4 108.0 418.4 ; C8 N9 C4
> 20 21 22 1 108.0 418.4 108.0 418.4 ; N9 C8 N7
> 21 22 23 1 108.0 418.4 108.0 418.4 ; C8 N7 C5
> 22 23 24 1 108.0 418.4 108.0 418.4 ; N7 C5 C4
> 22 23 28 1 132.0 418.4 132.0 418.4 ; N7 C5 C6
> 24 23 28 1 120.0 418.4 120.0 418.4 ; C4 C5 C6
> 20 24 23 1 108.0 418.4 108.0 418.4 ; N9 C4 C5
> 20 24 25 1 132.0 418.4 132.0 418.4 ; N9 C4 N3
> 23 24 25 1 120.0 418.4 120.0 418.4 ; C5 C4 N3
> 24 25 26 1 120.0 418.4 120.0 418.4 ; C4 N3 C2
> 25 26 27 1 120.0 418.4 120.0 418.4 ; N3 C2 N1
> 26 27 28 1 120.0 418.4 120.0 418.4 ; C2 N1 C6
> 23 28 27 1 120.0 418.4 120.0 418.4 ; C5 C6 N1
> 23 28 29 1 120.0 418.4 120.0 418.4 ; C5 C6 N6
> 27 28 29 1 120.0 418.4 120.0 418.4 ; N1 C6 N6
> 28 29 30 1 120.0 292.9 120.0 292.9 ; C6 N6 HAD
> 28 29 31 1 120.0 292.9 120.0 292.9 ; C6 N6 HAC
> 30 29 31 1 120.0 334.7 120.0 334.7 ; HAD N6 HAC
> [ dihedrals ]
> ;ai aj ak al fu c0 c1 m c0 c1 m
> 20 19 21 24 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI N9 C1* C8 C4
> 23 28 24 22 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C5 C6 C4 N7
> 24 25 23 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 N3 C5 N9
> 28 23 27 29 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C6 C5 N1 N6
> 29 28 30 31 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI N6 C6 HAD HAC
> 2 1 3 4 2 35.3 836.8 0 35.3 836.8 0 ; IDI PB O2B O3B O1B
> 6 5 8 7 2 35.3 836.8 0 35.3 836.8 0 ; IDI PA O3A O2A O1A
> 11 10 13 12 2 35.3 836.8 0 35.3 836.8 0 ; IDI C4* C5* C3* O4*
> 13 11 16 14 2 35.3 836.8 0 35.3 836.8 0 ; IDI C3* C4* C2* O3*
> 16 13 19 17 2 35.3 836.8 0 35.3 836.8 0 ; IDI C2* C3* C1* O2*
> 19 12 16 20 2 35.3 836.8 0 35.3 836.8 0 ; IDI C1* O4* C2* N9
> 20 21 22 23 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI N9 C8 N7 C5
> 21 22 23 24 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C8 N7 C5 C4
> 22 23 24 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI N7 C5 C4 N9
> 23 24 20 21 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C5 C4 N9 C8
> 24 20 21 22 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 N9 C8 N7
> 23 24 25 26 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C5 C4 N3 C2
> 24 25 26 27 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 N3 C2 N1
> 25 26 27 28 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI N3 C2 N1 C6
> 26 27 28 23 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C2 N1 C6 C5
> 27 28 23 24 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI N1 C6 C5 C4
> 28 23 24 25 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C6 C5 C4 N3
> 6 5 2 1 1 0.0 1.0 3 0.0 1.0 3 ; DI PA O3A PB O2B
> 6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; DI PA O3A PB O2B
> 2 5 6 9 1 0.0 1.0 3 0.0 1.0 3 ; DI PB O3A PA O5*
> 2 5 6 9 1 0.0 3.1 2 0.0 3.1 2 ; DI PB O3A PA O5*
> 10 9 6 5 1 0.0 1.0 3 0.0 1.0 3 ; DI C5* O5* PA O3A
> 10 9 6 5 1 0.0 3.1 2 0.0 3.1 2 ; DI C5* O5* PA O3A
> 6 9 10 11 1 0.0 3.8 3 0.0 3.8 3 ; DI PA O5* C5* C4*
> 13 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; DI C3* C4* C5* O5*
> 10 11 12 19 1 0.0 3.8 3 0.0 3.8 3 ; DI C5* C4* O4* C1*
> 10 11 13 16 1 0.0 5.9 3 0.0 5.9 3 ; DI C5* C4* C3* C2*
> 20 19 12 11 1 0.0 3.8 3 0.0 3.8 3 ; DI N9 C1* O4* C4*
> 11 13 14 15 1 0.0 1.3 3 0.0 1.3 3 ; DI C4* C3* O3* HAA
> 19 16 13 11 1 0.0 5.9 3 0.0 5.9 3 ; DI C1* C2* C3* C4*
> 13 16 17 18 1 0.0 1.3 3 0.0 1.3 3 ; DI C3* C2* O2* HAB
> 13 16 19 20 1 0.0 5.9 3 0.0 5.9 3 ; DI C3* C2* C1* N9
> 12 19 20 24 1 0.0 0.0 2 0.0 0.0 2 ; DI O4* C1* N9 C4
> 23 28 29 31 1 180.0 33.5 2 180.0 33.5 2 ; DI C5 C6 N6 HAC
>
> ###########################################################################
>
>
> Best Regard!
> Zhiguo Liu
> DDDC
> Chinese Academy of Science
> Shanghai,China
> zgliu at iris3.simm.ac.cn
> 2004-03-14
>
>
>
>
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##############################################################################
Dr. Daan van Aalten Wellcome Trust RCD Fellow / Reader
Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
School of Life Sciences E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk
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