[gmx-users] itp problem

[Justin Lemkul]

On 8/18/13 2:57 AM, Albert wrote:
> Hello:
>
>   I am trying to restrain part  of my protein. First I generate a index file by
> make_ndx. Then I use genrest for this purpose like:
>
> genres -f npt.gro -o helix -n -fc 400
>
> after that I change the following in the topol.top file, like:
>
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "helix.itp"
> #endif
>
> when I run grompp, it claimed following warnings:
>
> WARNING 1 [file helix.itp, line 1]:
>    Too few parameters on line (source file
>    /home/albert/install/source/gromacs-4.6.3/src/kernel/toppush.c, line 1756)
>
> here is my helix.itp:
> ; position restraints for System of
>
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     5    1        400        400        400
>    24    1        400        400        400
>    41    1        400        400        400
>    48    1        400        400        400
>    59    1        400        400        400
>    70    1        400        400        400
>    86    1        400        400        400
>   107    1        400        400        400
>   126    1        400        400        400
>   140    1        400        400        400
>   156    1        400        400        400
>   171    1        400        400        400
>   190    1        400        400        400
>   200    1        400        400        400
>   219    1        400        400        400
>   229    1        400        400        400
>   245    1        400        400        400
>   264    1        400        400        400
>   274    1        400        400        400
>
>

Does replacing "helix.itp" with the original "posre.itp" from pdb2gmx fix the 
problem?  I see no reason why this file would cause problems, especially if it 
was generated by genrestr, so it is important to test whether the original 
topology works correctly to verify the structure and validity of your #include 
statements.

-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 | (410) 706-7441

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