[gmx-users] Self made GDP topology file.......deforms severely with LINC warning during EM and stopped
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Thu Nov 4 19:34:57 CET 2004
Hi Zhenting
You cannot use PRODRG topologies for anything else than the ffgmx
forcefield. If you start editing them it is not too difficult to make some
mistakes and obtain the deformed structure.
We plan to, before Xmas, release a freely downloadable version of PRODRG
which can also write out gromos96 topologies.
cheers
Daan
On Fri, 5 Nov 2004, Zhenting Gao wrote:
> Hi gmx-users,
>
> A GDP is in my protein complex. So I made my own Gromos 96 FF topology file for GDP.
> First, I get the topology from PRODRG server.
> Then I use Gaussian to recalculate the atom charge.
> At last I refer to the topology of ATP and GUA in ffG43a1.rtp to modify the topology file for GDP.
> However, the GDP deforms severely during the EM, and even crashes if I run a heating process.(it deforms whether I add positive ion or not. )
> In contrast, the topology files generated by pdb2gmx for ATP and DGUA make the structure ramain good during a 300K heating process.
> Why it deforms? It is the wrong force parameter? Or the wrong atom charge?
>
> Please help me to check. The topology files are listed as below.
>
> Thanks.
>
> GDP.gro
> -------------------------------------------------------------------------------
> PRODRG COORDS
> 33
> 1GDP O2B 1 13.796 -0.791 5.821
> 1GDP PB 2 13.911 -0.692 5.803
> 1GDP O3B 3 14.047 -0.756 5.808
> 1GDP O1B 4 13.899 -0.581 5.703
> 1GDP O3A 5 13.903 -0.603 5.936
> 1GDP PA 6 13.884 -0.674 6.079
> 1GDP O1A 7 13.832 -0.817 6.074
> 1GDP O2A 8 14.009 -0.643 6.156
> 1GDP O5' 9 13.765 -0.580 6.127
> 1GDP C5' 10 13.801 -0.458 6.192
> 1GDP C4' 11 13.672 -0.403 6.247
> 1GDP O4' 12 13.568 -0.441 6.158
> 1GDP C3' 13 13.636 -0.465 6.382
> 1GDP O3' 14 13.660 -0.381 6.493
> 1GDP HAA 15 13.759 -0.370 6.506
> 1GDP C2' 16 13.487 -0.474 6.373
> 1GDP O2' 17 13.439 -0.353 6.433
> 1GDP HAB 18 13.339 -0.352 6.431
> 1GDP C1' 19 13.448 -0.469 6.227
> 1GDP N9 20 13.387 -0.597 6.187
> 1GDP C8 21 13.442 -0.705 6.127
> 1GDP N7 22 13.347 -0.801 6.108
> 1GDP C5 23 13.232 -0.754 6.159
> 1GDP C4 24 13.259 -0.620 6.214
> 1GDP N3 25 13.162 -0.549 6.273
> 1GDP C2 26 13.036 -0.595 6.285
> 1GDP N2 27 12.943 -0.515 6.342
> 1GDP HAE 28 12.968 -0.423 6.373
> 1GDP HAD 29 12.848 -0.547 6.352
> 1GDP N1 30 13.002 -0.717 6.239
> 1GDP HAC 31 12.907 -0.748 6.248
> 1GDP C6 32 13.093 -0.798 6.183
> 1GDP O6 33 13.058 -0.909 6.144
> -------------------------------------------------------------------------------
> GDP.top
> -------------------------------------------------------------------------------
> ; This file is modified to Gromos 96 FF on 20041104
> ;
> ; This file was generated by PRODRG version 041015.0515
> ; PRODRG written/copyrighted by Daan van Aalten
> ;
> ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> ;
> ; When using this software in a publication, cite:
> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> ; PRODRG - a tool for high-throughput crystallography
> ; of protein-ligand complexes.
> ; Acta Crystallogr. D60, 1355--1363.
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> [ moleculetype ]
> ; Name nrexcl
> GDP 3
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OM 1 GDP O2B 1 -0.941 15.9994
> 2 P 1 GDP PB 1 1.334 30.9738
> 3 OM 1 GDP O3B 1 -0.975 15.9994
> 4 OM 1 GDP O1B 1 -1.043 15.9994
> 5 OA 1 GDP O3A 2 -0.482 15.9994
> 6 P 1 GDP PA 2 1.429 30.9738
> 7 OM 1 GDP O1A 2 -0.852 15.9994
> 8 OM 1 GDP O2A 2 -0.949 15.9994
> 9 OA 1 GDP O5' 2 -0.672 15.9994
> 10 CH2 1 GDP C5' 3 0.179 14.0270
> 11 CH1 1 GDP C4' 3 0.362 13.0190
> 12 OA 1 GDP O4' 3 -0.412 15.9994
> 13 CH1 1 GDP C3' 4 0.233 13.0190
> 14 OA 1 GDP O3' 4 -0.710 15.9994
> 15 H 1 GDP HAA 4 0.399 1.0080
> 16 CH1 1 GDP C2' 5 0.419 13.0190
> 17 OA 1 GDP O2' 5 -0.686 15.9994
> 18 H 1 GDP HAB 5 0.357 1.0080
> 19 CH1 1 GDP C1' 5 0.140 13.0190
> 20 NR 1 GDP N9 6 0.113 14.0067
> 21 CR1 1 GDP C8 6 0.354 13.0190
> 22 NR 1 GDP N7 7 -0.497 14.0067
> 23 C 1 GDP C5 7 -0.025 12.0110
> 24 C 1 GDP C4 7 0.245 12.0110
> 25 NR 1 GDP N3 7 -0.822 14.0067
> 26 C 1 GDP C2 7 1.075 12.0110
> 27 NT 1 GDP N2 8 -1.184 14.0067
> 28 H 1 GDP HAE 8 0.475 1.0080
> 29 H 1 GDP HAD 8 0.454 1.0080
> 30 NR 1 GDP N1 9 -0.791 14.0067
> 31 H 1 GDP HAC 9 0.403 1.0080
> 32 C 1 GDP C6 9 0.749 12.0110
> 33 O 1 GDP O6 9 -0.679 15.9994
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 2 gb_23 ;0.161 251040.0 0.161 251040.0 ; O2B PB
> 2 3 2 gb_23 ;0.161 251040.0 0.161 251040.0 ; PB O3B
> 2 4 2 gb_23 ;0.148 376560.0 0.148 376560.0 ; PB O1B
> 2 5 2 gb_27 ;0.161 251040.0 0.161 251040.0 ; PB O3A
> 5 6 2 gb_27 ;0.161 251040.0 0.161 251040.0 ; O3A PA
> 6 7 2 gb_23 ;0.148 376560.0 0.148 376560.0 ; PA O1A
> 6 8 2 gb_23 ;0.148 376560.0 0.148 376560.0 ; PA O2A
> 6 9 2 gb_27 ;0.161 251040.0 0.161 251040.0 ; PA O5'
> 9 10 2 gb_19 ;0.143 251040.0 0.143 251040.0 ; O5' C5'
> 10 11 2 gb_25 ;0.153 251040.0 0.153 251040.0 ; C5' C4'
> 11 12 2 gb_19 ;0.144 251040.0 0.144 251040.0 ; C4' O4'
> 11 13 2 gb_25 ;0.153 334720.0 0.153 334720.0 ; C4' C3'
> 12 19 2 gb_19 ;0.144 251040.0 0.144 251040.0 ; O4' C1'
> 13 14 2 gb_19 ;0.143 334720.0 0.143 334720.0 ; C3' O3'
> 13 16 2 gb_25 ;0.153 334720.0 0.153 334720.0 ; C3' C2'
> 14 15 2 gb_1 ;0.100 313800.0 0.100 313800.0 ; O3' HAA
> 16 17 2 gb_19 ;0.143 334720.0 0.143 334720.0 ; C2' O2'
> 16 19 2 gb_25 ;0.153 334720.0 0.153 334720.0 ; C2' C1'
> 17 18 2 gb_1 ;0.100 313800.0 0.100 313800.0 ; O2' HAB
> 19 20 2 gb_21 ;0.148 251040.0 0.148 251040.0 ; C1' N9
> 20 21 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; N9 C8
> 20 24 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; N9 C4
> 21 22 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; C8 N7
> 22 23 2 gb_9 ;0.133 418400.0 0.133 418400.0 ; N7 C5
> 23 24 2 gb_15 ;0.139 418400.0 0.139 418400.0 ; C5 C4
> 23 32 2 gb_15 ;0.139 418400.0 0.139 418400.0 ; C5 C6
> 24 25 2 gb_11 ;0.134 418400.0 0.134 418400.0 ; C4 N3
> 25 26 2 gb_11 ;0.134 418400.0 0.134 418400.0 ; N3 C2
> 26 27 2 gb_8 ;0.133 376560.0 0.133 376560.0 ; C2 N2
> 26 30 2 gb_16 ;0.140 334720.0 0.140 334720.0 ; C2 N1
> 27 28 2 gb_2 ;0.100 374468.0 0.100 374468.0 ; N2 HAE
> 27 29 2 gb_2 ;0.100 374468.0 0.100 374468.0 ; N2 HAD
> 30 31 2 gb_2 ;0.100 374468.0 0.100 374468.0 ; N1 HAC
> 30 32 2 gb_16 ;0.140 334720.0 0.140 334720.0 ; N1 C6
> 32 33 2 gb_4 ;0.123 502080.0 0.123 502080.0 ; C6 O6
> [ 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 32 1 ; N9 C6
> 21 25 1 ; C8 N3
> 21 32 1 ; C8 C6
> 22 25 1 ; N7 N3
> 22 30 1 ; N7 N1
> 22 33 1 ; N7 O6
> 23 26 1 ; C5 C2
> 23 31 1 ; C5 HAC
> 24 27 1 ; C4 N2
> 24 30 1 ; C4 N1
> 24 33 1 ; C4 O6
> 25 28 1 ; N3 HAE
> 25 29 1 ; N3 HAD
> 25 31 1 ; N3 HAC
> 25 32 1 ; N3 C6
> 26 33 1 ; C2 O6
> 27 31 1 ; N2 HAC
> 27 32 1 ; N2 C6
> 28 30 1 ; HAE N1
> 29 30 1 ; HAD N1
> 31 33 1 ; HAC O6
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 2 ga_13 ;103.0 397.5 103.0 397.5 ; O2B PB O3B
> 1 2 4 2 ga_13 ;109.6 397.5 109.6 397.5 ; O2B PB O1B
> 1 2 5 2 ga_13 ;103.0 397.5 103.0 397.5 ; O2B PB O3A
> 3 2 4 2 ga_13 ;109.6 397.5 109.6 397.5 ; O3B PB O1B
> 3 2 5 2 ga_13 ;103.0 397.5 103.0 397.5 ; O3B PB O3A
> 4 2 5 2 ga_13 ;109.6 397.5 109.6 397.5 ; O1B PB O3A
> 2 5 6 2 ga_25 ;120.0 397.5 120.0 397.5 ; PB O3A PA
> 5 6 7 2 ga_13 ;109.6 397.5 109.6 397.5 ; O3A PA O1A
> 5 6 8 2 ga_13 ;109.6 397.5 109.6 397.5 ; O3A PA O2A
> 5 6 9 2 ga_4 ;103.0 397.5 103.0 397.5 ; O3A PA O5'
> 7 6 8 2 ga_28 ;120.0 585.8 120.0 585.8 ; O1A PA O2A
> 7 6 9 2 ga_13 ;109.6 397.5 109.6 397.5 ; O1A PA O5'
> 8 6 9 2 ga_13 ;109.6 397.5 109.6 397.5 ; O2A PA O5'
> 6 9 10 2 ga_25 ;120.0 397.5 120.0 397.5 ; PA O5' C5'
> 9 10 11 2 ga_8 ;111.0 460.2 111.0 460.2 ; O5' C5' C4'
> 10 11 12 2 ga_8 ;109.5 284.5 109.5 284.5 ; C5' C4' O4'
> 10 11 13 2 ga_7 ;109.5 251.0 109.5 251.0 ; C5' C4' C3'
> 12 11 13 2 ga_8 ;104.0 460.2 104.0 460.2 ; O4' C4' C3'
> 11 12 19 2 ga_9 ;104.0 460.2 104.0 460.2 ; C4' O4' C1'
> 11 13 14 2 ga_8 ;109.5 460.2 109.5 460.2 ; C4' C3' O3'
> 11 13 16 2 ga_7 ;104.0 460.2 104.0 460.2 ; C4' C3' C2'
> 14 13 16 2 ga_8 ;109.5 460.2 109.5 460.2 ; O3' C3' C2'
> 13 14 15 2 ga_11 ;109.5 397.5 109.5 397.5 ; C3' O3' HAA
> 13 16 17 2 ga_8 ;109.5 460.2 109.5 460.2 ; C3' C2' O2'
> 13 16 19 2 ga_7 ;104.0 460.2 104.0 460.2 ; C3' C2' C1'
> 17 16 19 2 ga_8 ;109.5 460.2 109.5 460.2 ; O2' C2' C1'
> 16 17 18 2 ga_11 ;109.5 397.5 109.5 397.5 ; C2' O2' HAB
> 12 19 16 2 ga_8 ;104.0 460.2 104.0 460.2 ; O4' C1' C2'
> 12 19 20 2 ga_8 ;109.5 284.5 109.5 284.5 ; O4' C1' N9
> 16 19 20 2 ga_8 ;109.5 284.5 109.5 284.5 ; C2' C1' N9
> 19 20 21 2 ga_36 ;126.0 418.4 126.0 418.4 ; C1' N9 C8
> 19 20 24 2 ga_36 ;126.0 418.4 126.0 418.4 ; C1' N9 C4
> 21 20 24 2 ga_6 ;108.0 418.4 108.0 418.4 ; C8 N9 C4
> 20 21 22 2 ga_6 ;108.0 418.4 108.0 418.4 ; N9 C8 N7
> 21 22 23 2 ga_6 ;108.0 418.4 108.0 418.4 ; C8 N7 C5
> 22 23 24 2 ga_6 ;108.0 418.4 108.0 418.4 ; N7 C5 C4
> 22 23 32 2 ga_38 ;132.0 418.4 132.0 418.4 ; N7 C5 C6
> 24 23 32 2 ga_26 ;120.0 418.4 120.0 418.4 ; C4 C5 C6
> 20 24 23 2 ga_6 ;108.0 418.4 108.0 418.4 ; N9 C4 C5
> 20 24 25 2 ga_38 ;132.0 418.4 132.0 418.4 ; N9 C4 N3
> 23 24 25 2 ga_26 ;120.0 418.4 120.0 418.4 ; C5 C4 N3
> 24 25 26 2 ga_26 ;120.0 418.4 120.0 418.4 ; C4 N3 C2
> 25 26 27 2 ga_26 ;120.0 418.4 120.0 418.4 ; N3 C2 N2
> 25 26 30 2 ga_26 ;120.0 418.4 120.0 418.4 ; N3 C2 N1
> 27 26 30 2 ga_26 ;120.0 418.4 120.0 418.4 ; N2 C2 N1
> 26 27 28 2 ga_22 ;120.0 292.9 120.0 292.9 ; C2 N2 HAE
> 26 27 29 2 ga_22 ;120.0 292.9 120.0 292.9 ; C2 N2 HAD
> 28 27 29 2 ga_23 ;120.0 334.7 120.0 334.7 ; HAE N2 HAD
> 26 30 31 2 ga_24 ;120.0 376.6 120.0 376.6 ; C2 N1 HAC
> 26 30 32 2 ga_26 ;120.0 418.4 120.0 418.4 ; C2 N1 C6
> 31 30 32 2 ga_24 ;120.0 376.6 120.0 376.6 ; HAC N1 C6
> 23 32 30 2 ga_26 ;120.0 418.4 120.0 418.4 ; C5 C6 N1
> 23 32 33 2 ga_26 ;120.0 418.4 120.0 418.4 ; C5 C6 O6
> 30 32 33 2 ga_26 ;120.0 418.4 120.0 418.4 ; N1 C6 O6
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 19 21 24 20 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N9 C1' C8 C4
> 32 24 22 23 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C5 C6 C4 N7
> 25 23 20 24 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C4 N3 C5 N9
> 25 30 27 26 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C2 N3 N1 N2
> 26 28 29 27 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N2 C2 HAE HAD
> 32 31 26 30 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N1 C6 HAC C2
> 23 30 33 32 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C6 C5 N1 O6
> 1 4 3 2 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp PB O2B O1B O3B
> 5 8 7 6 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp PA O3A O2A O1A
> 10 13 12 11 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C4' C5' C3' O4'
> 11 16 14 13 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C3' C4' C2' O3'
> 13 19 17 16 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C2' C3' C1' O2'
> 12 16 20 19 2 gi_2 ; 35.3 836.8 0 35.3 836.8 0 ; imp C1' O4' C2' N9
> 21 22 23 20 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N9 C8 N7 C5
> 22 23 24 21 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C8 N7 C5 C4
> 23 24 20 22 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N7 C5 C4 N9
> 24 20 21 23 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C5 C4 N9 C8
> 20 21 22 24 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C4 N9 C8 N7
> 24 25 26 23 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C5 C4 N3 C2
> 25 26 30 24 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C4 N3 C2 N1
> 26 30 32 25 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N3 C2 N1 C6
> 30 32 23 26 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C2 N1 C6 C5
> 32 23 24 30 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp N1 C6 C5 C4
> 23 24 25 32 2 gi_1 ; 0.0 1673.6 0 0.0 1673.6 0 ; imp C6 C5 C4 N3
> 5 2 1 6 1 gd_11 ; 0.0 1.0 3 0.0 1.0 3 ; dih PA O3A PB O2B
> 5 2 1 6 1 gd_9 ; 0.0 3.1 2 0.0 3.1 2 ; dih PA O3A PB O2B
> 5 6 9 2 1 gd_11 ; 0.0 1.0 3 0.0 1.0 3 ; dih PB O3A PA O5'
> 5 6 9 2 1 gd_9 ; 0.0 3.1 2 0.0 3.1 2 ; dih PB O3A PA O5'
> 9 6 5 10 1 gd_9 ; 0.0 1.0 3 0.0 1.0 3 ; dih C5' O5' PA O3A
> 9 6 5 10 1 gd_11 ; 0.0 3.1 2 0.0 3.1 2 ; dih C5' O5' PA O3A
> 9 10 11 6 1 gd_14 ; 0.0 3.8 3 0.0 3.8 3 ; dih PA O5' C5' C4'
> 11 10 9 13 1 gd_7 ; 0.0 5.9 3 0.0 5.9 3 ; dih C3' C4' C5' O5'
> 11 12 19 10 1 gd_14 ; 0.0 3.8 3 0.0 3.8 3 ; dih C5' C4' O4' C1'
> 11 13 16 10 1 gd_17 ; 0.0 5.9 3 0.0 5.9 3 ; dih C5' C4' C3' C2'
> 19 12 11 20 1 gd_14 ; 0.0 3.8 3 0.0 3.8 3 ; dih N9 C1' O4' C4'
> 13 14 15 11 1 gd_12 ; 0.0 1.3 3 0.0 1.3 3 ; dih C4' C3' O3' HAA
> 16 13 11 19 1 gd_17 ; 0.0 5.9 3 0.0 5.9 3 ; dih C1' C2' C3' C4'
> 16 17 18 13 1 gd_12 ; 0.0 1.3 3 0.0 1.3 3 ; dih C3' C2' O2' HAB
> 16 19 20 13 1 gd_7 ; 0.0 5.9 3 0.0 5.9 3 ; dih C3' C2' C1' N9
> 19 20 24 12 1 gd_6 ; 0.0 0.0 2 0.0 0.0 2 ; dih O4' C1' N9 C4
> 26 27 29 25 1 gd_4 ;180.0 33.5 2 180.0 33.5 2 ; dih N3 C2 N2 HAD
> ; Include Position restraint file
> #ifdef POSRES_GDP
> #include "posre_gdp.itp"
> #endif
> ; Include water topology
> #include "spc.itp"
> ; Include generic topology for ions
> #include "ions.itp"
> [ system ]
> ; Name
> GDP in water
> [ molecules ]
> ; Compound #mols
> GDP 1
> SOL 1838
> -------------------------------------------------------------------------------
> EM_gdp.mdp
> -------------------------------------------------------------------------------
> title = mitwasser
> cpp = /lib/cpp
> define = -DFLEXIBLE -DPOSRES_GDP
> constraints = none
> integrator = l-bfgs
> dt = 0.002 ; ps !
> nsteps = 5000
> nstlist = 5 ;originally this is set to 10
> ns_type = grid
> coulombtype = Switch
> vdw-type = Switch
> rlist = 1.2
> rcoulomb = 1.0
> rvdw = 1.0
> ;http://www.gromacs.org/pipermail/gmx-users/2004-May/010608.html
> ; Energy minimizing stuff
> ;
> emtol = 10.0
> emstep = 0.01
> epsilon_r = 1
> -------------------------------------------------------------------------------
> Deformed_gdp.pdb
> -------------------------------------------------------------------------------
> HEADER GDP in water
> MODEL 1
> ATOM 1 O2B GDP 1 24.340 16.030 15.246 1.00 0.00
> ATOM 2 PB GDP 1 25.390 17.010 15.440 1.00 0.00
> ATOM 3 O3B GDP 1 26.840 16.840 15.446 1.00 0.00
> ATOM 4 O1B GDP 1 25.250 18.190 14.580 1.00 0.00
> ATOM 5 O3A GDP 1 24.990 17.830 16.606 1.00 0.00
> ATOM 6 PA GDP 1 25.280 16.740 17.586 1.00 0.00
> ATOM 7 O1A GDP 1 24.060 16.120 18.146 1.00 0.00
> ATOM 8 O2A GDP 1 26.540 16.800 18.360 1.00 0.00
> ATOM 9 O5' GDP 1 25.050 17.730 18.860 1.00 0.00
> ATOM 10 C5' GDP 1 24.480 19.060 18.866 1.00 0.00
> ATOM 11 C4' GDP 1 23.090 18.920 19.460 1.00 0.00
> ATOM 12 O4' GDP 1 22.040 18.880 18.480 1.00 0.00
> ATOM 13 C3' GDP 1 22.690 19.970 20.500 1.00 0.00
> ATOM 14 O3' GDP 1 23.340 19.900 21.820 1.00 0.00
> ATOM 15 HAA GDP 1 24.330 20.130 21.720 1.00 0.00
> ATOM 16 C2' GDP 1 21.150 19.890 20.280 1.00 0.00
> ATOM 17 O2' GDP 1 20.310 19.760 21.440 1.00 0.00
> ATOM 18 HAB GDP 1 19.750 20.600 21.480 1.00 0.00
> ATOM 19 C1' GDP 1 21.070 18.600 19.480 1.00 0.00
> ATOM 20 N9 GDP 1 20.040 17.610 19.046 1.00 0.00
> ATOM 21 C8 GDP 1 20.430 16.580 18.280 1.00 0.00
> ATOM 22 N7 GDP 1 19.510 15.630 18.286 1.00 0.00
> ATOM 23 C5 GDP 1 18.500 16.110 19.046 1.00 0.00
> ATOM 24 C4 GDP 1 18.770 17.430 19.526 1.00 0.00
> ATOM 25 N3 GDP 1 17.600 18.240 20.140 1.00 0.00
> ATOM 26 C2 GDP 1 16.620 17.910 19.380 1.00 0.00
> ATOM 27 N2 GDP 1 16.220 18.220 20.286 1.00 0.00
> ATOM 28 HAE GDP 1 17.430 18.290 20.226 1.00 0.00
> ATOM 29 HAD GDP 1 15.300 18.360 20.706 1.00 0.00
> ATOM 30 N1 GDP 1 16.200 16.710 19.266 1.00 0.00
> ATOM 31 HAC GDP 1 15.320 16.520 19.640 1.00 0.00
> ATOM 32 C6 GDP 1 17.140 15.770 19.166 1.00 0.00
> ATOM 33 O6 GDP 1 16.710 14.660 19.460 1.00 0.00
> TER 34 GDP 1
> ENDMDL
> END
> -------------------------------------------------------------------------------¡¡¡¡¡¡¡¡¡¡¡¡¡¡
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
>
> Yours sincerely,
> Zhenting Gao
> zhentg at 163.com
> 2004-11-3
>
> ------------------------------------
> Drug Discovery and Design Center,
> Shanghai Institute of Materia Medica,
> Chinese Academy of Science
> P.R. China
> URL http://www.dddc.ac.cn/group/zhentg.htm
>
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