[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Thu Sep 12 19:17:27 CEST 2013
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.
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).
Thanks Justin .., I appreciate your help for whole week. I stopped here
(give up).
--Rama
_______________________________________________________
Ramakrishna Koppisetti | Research Specialist | Protein NMR group |
Biochemistry Department | University of Missouri | Columbia, USA |
Email Id : koppisettir at missouri.edu | Mobile No : +573-529-5932 |
_______________________________________________________
On Thu, Sep 12, 2013 at 11:27 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote:
>
>> Hi,
>> These are the parameters I kept in the .rtp file for DMPC molecule. Still
>> getting same error message should I need to look at somewhere else.
>>
>> [ bondedtypes ]
>> ; Col 1: Type of bond
>> ; Col 2: Type of angles
>> ; Col 3: Type of proper dihedrals
>> ; Col 4: Type of improper dihedrals
>> ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
>> ; Col 6: Number of excluded neighbors for nonbonded interactions
>> ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
>> ; Col 8: Remove propers over the same bond as an improper if it is 1
>> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
>> 1 1 3 1 1 3 1 0
>>
>>
>> [ DMPC ]
>> [ atoms ]
>> ; name type charge chgnr
>> CN1 LC3 0.4000 1
>> CN2 LC3 0.4000 1
>> CN3 LC3 0.4000 1
>> NTM LNL -0.5000 1
>> CA LH2 0.3000 1
>> CB LC2 0.4000 2
>> OA LOS -0.8000 2
>> P LP 1.7000 2
>> OB LOM -0.8000 2
>> OC LOM -0.8000 2
>> OD LOS -0.7000 2
>> [ bonds ]
>> ; ai aj
>> CN1 NTM
>> CN2 NTM
>> CN3 NTM
>> NTM CA
>> CA CB
>> CB OA
>> OA P
>> P OB
>> P OC
>> P OD
>> OD CC
>> CC CD
>> CD OE
>> CD CE
>> OE C1A
>>
>
> If you don't specify bond lengths and force constants here, they need to
> be present in ffbonded.itp. Either approach is fine. The only issue you
> had before was that you included a function type, which would have
> explained the error you got before.
>
>
> [ angles ]
>> ; ai aj ak funct angle fc
>> CN1 NTM CN2 2 109.50 520.00
>> CN1 NTM CN3 2 109.50 520.00
>> CN1 NTM CA 2 109.50 520.00
>> CN2 NTM CN3 2 109.50 520.00
>> CN2 NTM CA 2 109.50 520.00
>> CN3 NTM CA 2 109.50 520.00
>> NTM CA CB 2 111.00 530.00
>> CA CB OA 2 111.00 530.00
>> CB OA P 2 120.00 530.00
>> OA P OC 2 109.60 450.00
>> OA P OB 2 109.60 450.00
>> OA P OD 2 103.00 420.00
>> P OD CC 2 120.00 530.00
>> OC P OB 2 120.00 780.00
>> OC P OD 2 109.60 450.00
>>
>
> Same as with [bonds], you cannot have a function type specified here.
>
>
> [ dihedrals ]
>> ; ai aj ak al funct ph0 cp mult
>> CN3 NTM CA CB 1 0.00 3.77 3
>> NTM CA CB OA 1 0.00 8.62 3
>> CA CB OA P 1 0.00 3.77 3
>> CB OA P OD 1 0.00 3.19 3
>> OA P OD CC 1 0.00 3.19 3
>> P OD CC CD 1 0.00 3.77 3
>> OD CC CD CE 1 0.00 5.92 3
>> CC CD OE C1A 1 0.00 3.77 3
>> CC CD CE OG 1 0.00 5.92 3
>> CD OE C1A C1B 1 180.00 24.00 2
>> CD CE OG C2A 1 0.00 3.77 3
>> OE C1A C1B C1C 1 0.00 1.00 6
>> [ impropers ]
>> ; GROMOS improper dihedrals
>> ; ai aj ak al funct angle fc
>> CD OE CE CC 2 35.26 334.72
>> C1A OE OF C1B 2 0.00 167.36
>> C2A OG OH C2B 2 0.00 167.36
>>
>>
> Same applies for the dihedrals and impropers.
>
> To avoid another string of incomplete replies, please answer the following
> questions directly. Remember, I'm trying (very hard) to help you resolve
> this and we're just spinning our wheels.
>
> 1. Did you re-run pdb2gmx after modifying the .rtp file?
> 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:
>
> atom_i atom_j funct b0 kb
>
> Anything more or less (in this case) is wrong. Can you identify any
> problematic lines, and if so, to which atoms do they apply?
>
>
> -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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