[gmx-users] Simulation with nbutanol

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 24 03:50:50 CEST 2012



On 4/23/12 9:47 PM, Juliana Angeiras wrote:
> Hello,
> I'm trying to build a box with nbutanol using the residue below for nbutanol
> (But), added in ffoplsaa.rtp
> ; Butanol
> [ But ]
> [ atoms ]
> ;
> C1 opls_135 -0.18 1
> H11 opls_140 0.06 1
> H12 opls_140 0.06 1
> H13 opls_140 0.06 1
> C2 opls_136 -0.12 2
> H21 opls_140 0.06 2
> H22 opls_140 0.06 2
> C3 opls_136 -0.12 3
> H31 opls_140 0.06 3
> H32 opls_140 0.06 3
> C4 opls_157 0.145 4
> H41 opls_140 0.06 4
> H42 opls_140 0.06 4
> OH opls_154 -0.683 4
> HO opls_155 0.418 4
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> C1 H11
> C1 H12
> C1 H13
> C1 C2
> C2 H21
> C2 H22
> C2 C3
> C3 H31
> C3 H32
> C3 C4
> C4 H41
> C4 H42
> C4 OH
> OH HO
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> H11 C1 H12
> H11 C1 H13
> H11 C1 C2
> H12 C1 H13
> H12 C1 C2
> H13 C1 C2
> C1 C2 H21
> C1 C2 H22
> C1 C2 C3
> H21 C2 H22
> H21 C2 C3
> H22 C2 C3
> C2 C3 H31
> C2 C3 H32
> C2 C3 C4
> H31 C3 H32
> H31 C3 C4
> H32 C3 C4
> C3 C4 H41
> C3 C4 H42
> C3 C4 OH
> H41 C4 H42
> H41 C4 OH
> H42 C4 OH
> C4 OH HO
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3 c4 c5
> H11 C1 C2 H21
> H11 C1 C2 H22
> H11 C1 C2 C3
> H12 C1 C2 H21
> H12 C1 C2 H22
> H12 C1 C2 C3
> H13 C1 C2 H21
> H13 C1 C2 H22
> H13 C1 C2 C3
> C1 C2 C3 H31
> C1 C2 C3 H32
> C1 C2 C3 C4
> H21 C2 C3 H31
> H21 C2 C3 H32
> H21 C2 C3 C4
> H22 C2 C3 H31
> H22 C2 C3 H32
> H22 C2 C3 C4
> C2 C3 C4 H41
> C2 C3 C4 H42
> C2 C3 C4 OH
> H31 C3 C4 H41
> H31 C3 C4 H42
> H31 C3 C4 OH
> H32 C3 C4 H41
> H32 C3 C4 H42
> H32 C3 C4 OH
> C3 C4 OH HO
> H41 C4 OH HO
> H42 C4 OH HO
> The .gro file used is
> 15
> 1But C1 1 2.561 2.686 0.006
> 1But H11 2 2.470 2.721 -0.042
> 1But H12 3 2.576 2.582 -0.021
> 1But H13 4 2.544 2.690 0.114
> 1But C2 5 2.681 2.772 -0.034
> 1But H21 6 2.692 2.769 -0.143
> 1But H22 7 2.661 2.877 -0.008
> 1But C3 8 2.811 2.727 0.033
> 1But H31 9 2.799 2.730 0.141
> 1But H32 10 2.831 2.623 0.007
> 1But C4 11 2.932 2.813 -0.008
> 1But H41 12 2.947 2.810 -0.116
> 1But H42 13 2.916 2.917 0.020
> 1But OH 14 3.048 2.765 0.055
> 1But HO 15 3.122 2.816 0.026
> 2.75000 2.75000 2.75000
> The command line for obtaining the topology file:
> pdb2gmx -f nbutoh.gro -o nbutoh2.gro -p topol.top
> return the error message:
> Fatal error:
> Invalid line in nbutoh.gro for atom 1:
> 1But C1 1 2.561 2.686 0.006

Your .gro file needs a title line as its first line.  Then it should work.

> I have tried of different ways for obtaining the gro and the topology file,
> include using the pdb file below, butit still fails.

What is the error when using the .pdb file?

-Justin

> HETATM 1 C1 But 1 2.510 -0.293 0.000
> HETATM 2 H11 But 1 3.385 0.351 -0.000
> HETATM 3 H12 But 1 2.567 -0.931 0.878
> HETATM 4 H13 But 1 2.567 -0.931 -0.878
> HETATM 5 C2 But 1 1.222 0.528 -0.000
> HETATM 6 H21 But 1 1.212 1.180 0.871
> HETATM 7 H22 But 1 1.212 1.180 -0.871
> HETATM 8 C3 But 1 -0.036 -0.341 -0.000
> HETATM 9 H31 But 1 -0.041 -0.990 -0.873
> HETATM 10 H32 But 1 -0.041 -0.990 0.873
> HETATM 11 C4 But 1 -1.317 0.471 0.000
> HETATM 12 H41 But 1 -1.349 1.113 0.880
> HETATM 13 H42 But 1 -1.349 1.113 -0.880
> HETATM 14 OH But 1 -2.404 -0.419 0.000
> HETATM 15 HO Bu t 1 -3.209 0.066 0.000
> CONECT 1 2 3 4 5
> CONECT 2 1
> CONECT 3 1
> CONECT 4 1
> CONECT 5 1 6 7 8
> CONECT 6 5
> CONECT 7 5
> CONECT 8 5 9 10 11
> CONECT 9 8
> CONECT 10 8
> CONECT 11 8 12 13 14
> CONECT 12 11
> CONECT 13 11
> CONECT 14 11 15
> CONECT 15 14
> END
> Can you help me to solve my problem?
> Thanks,
> --
> Juliana Angeiras Batista da Silva
> Laboratório de Química Teórica e Computacional
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> 50740-540 Recife (PE) - Brazil
>
> Phone: +55 81 2126-8440 ext. 5007
> Phone: +55 81 9197-9297.
>
>

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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