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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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