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 fcxfcyfcz
51400400400
241400400400
411400400400
481400400400
591400400400
701400400400
861400400400
1071400400400
1261400400400
1401400400400
1561400400400
1711400400400
1901400400400
2001400400400
2191400400400
2291400400400
2451400400400
2641400400400
2741400400400
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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