[gmx-users] NMR restrained MD

[Justin Lemkul]

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

-- 
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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 | (410) 706-7441

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