[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Thu Sep 12 20:57:31 CEST 2013
Hi Justin,
Output topology from pdb2gmx. You could see some entries differ between
two molecules.
I'm looking forward to do restrained MD for this system by using Gromacs.
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 100 PHE rtp PHE q +1.0
1 opls_287 100 PHE N 1 -0.3 14.0067 ;
qtot -0.3
2 opls_290 100 PHE H1 1 0.33 1.008 ;
qtot 0.03
3 opls_290 100 PHE H2 1 0.33 1.008 ;
qtot 0.36
4 opls_290 100 PHE H3 1 0.33 1.008 ;
qtot 0.69
5 opls_293B 100 PHE CA 1 0.25 12.011 ;
qtot 0.94
6 opls_140 100 PHE HA 1 0.06 1.008 ;
qtot 1
7 opls_149 100 PHE CB 2 -0.005 12.011 ;
qtot 0.995
; residue 1 DMPC rtp DMPC q 0.0
2514 LC3 1 DMPC CN1 874 0.4 15.035 ;
qtot 8.4
2515 LC3 1 DMPC CN2 874 0.4 15.035 ;
qtot 8.8
2516 LC3 1 DMPC CN3 874 0.4 15.035 ;
qtot 9.2
2517 LNL 1 DMPC NTM 874 -0.5 14.0067 ;
qtot 8.7
2518 LH2 1 DMPC CA 874 0.3 14.027 ;
qtot 9
2519 LC2 1 DMPC CB 875 0.4 14.027 ;
qtot 9.4
2520 LOS 1 DMPC OA 875 -0.8 15.9994 ;
qtot 8.6
2521 LP 1 DMPC P 875 1.7 30.9738 ;
qtot 10.3
2522 LOM 1 DMPC OB 875 -0.8 15.9994 ;
qtot 9.5
2523 LOM 1 DMPC OC 875 -0.8 15.9994 ;
qtot 8.7
2524 LOS 1 DMPC OD 875 -0.7 15.9994 ;
qtot 8
2525 LC2 1 DMPC CC 876 0.4 14.027 ;
qtot 8.4
2526 LH1 1 DMPC CD 876 0.3 13.019 ;
qtot 8.7
2527 LOS 1 DMPC OE 876 -0.7 15.9994 ;
qtot 8
[ bonds ]
; ai aj funct c0 c1 c2 c3
;bonds for protein
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 21 1
7 8 1
7 9 1
7 10 1
;bonds from lipid atoms
2514 2517 1 0.1470 8.7100e+06
2515 2517 1 0.1470 8.7100e+06
2516 2517 1 0.1470 8.7100e+06
2517 2518 1 0.1470 8.7100e+06
2518 2519 1 0.1530 7.1500e+06
2519 2520 1 0.1430 8.1800e+06
2520 2521 1 0.1610 4.8400e+06
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
1 10 1
1 22 1
1 23 1
2 6 1
2 7 1
2 21 1
3 6 1
3 7 1
3 21 1
4 6 1
4 7 1
4 21 1
5 11 1
5 13 1
[ angles ]
; ai aj ak funct c0 c1
c2 c3
;angles for protein atoms
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 21 1
6 5 7 1
6 5 21 1
;angles for lipid atoms
2514 2517 2515 1 109.50 520.00
2514 2517 2516 1 109.50 520.00
2514 2517 2518 1 109.50 520.00
2515 2517 2516 1 109.50 520.00
2515 2517 2518 1 109.50 520.00
2516 2517 2518 1 109.50 520.00
2517 2518 2519 1 111.00 530.00
2518 2519 2520 1 111.00 530.00
2519 2520 2521 1 120.00 530.00
2520 2521 2522 1 109.60 450.00
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
;For protein
2 1 5 6 3
2 1 5 7 3
2 1 5 21 3
23 25 27 30 3 dih_ARG_chi1_N_C_C_C
45 25 27 30 3 dih_ARG_chi1_C_C_C_CO
;For lipids
2516 2517 2518 2519 3 1 0.00 3.77 3
2514 2517 2518 2519 3
2515 2517 2518 2519 3
2517 2518 2519 2520 3 1 0.00 8.62 3
2518 2519 2520 2521 3 1 0.00 3.77 3
2519 2520 2521 2524 3 1 0.00 3.19 3
2519 2520 2521 2522 3
2519 2520 2521 2523 3
2520 2521 2524 2525 3 1 0.00 3.19 3
Thanks
--Rama
==========================================================
On Thu, Sep 12, 2013 at 12:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/12/13 1:17 PM, Rama Krishna Koppisetti wrote:
>
>> 1. Did you re-run pdb2gmx after modifying the .rtp file?
>>
>> Yes.. I do run with modified .rtp file but output was same as previous.
>>
>> 2. Have you looked into the [bonds] directive in the .top file that
>> pdb2gmx
>> created to see if anything is out of place? Every line should have 5
>> entries:
>>
>> [bonds] directive contains only 3 entries for every line.
>>
>> atom_i atom_j funct b0 kb
>>
>> the entries present in [bonds] directive in the .top file was
>>
>> atom_i atom_j funct c0 c1 c2 c3.
>>
>>
> This format suggests they are actually dihedrals. Can you provide some
> actual snippets of the .top (just copied and pasted so I can try to make
> sense of this. There is no reason that the .rtp entry you provided would
> yield this output.
>
>
> These are the some warnings for Zinc and calcium ions for pdb2gmx
>> Warning: Residue ZN264 in chain has different type (Ion) from starting
>> residue PHE100 (Protein).
>> Warning: Residue ZN265 in chain has different type (Ion) from starting
>> residue PHE100 (Protein).
>> Warning: Residue CA266 in chain has different type (Ion) from starting
>> residue PHE100 (Protein).
>> Warning: Residue CA267 in chain has different type (Ion) from starting
>> residue PHE100 (Protein).
>> Warning: Residue CA268 in chain has different type (Ion) from starting
>> residue PHE100 (Protein).
>>
>>
> Not an issue, given your merging scheme. Normally, pdb2gmx expects only
> atoms belonging to similar chemical entities (protein, nucleic acid, ions,
> etc) to be in separate moleculetypes.
>
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
> --
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