[gmx-users] about trp_drug_tutor

Li Jiang jiang-li at ims.ac.jp
Thu Oct 14 10:28:28 CEST 2004

hi all,
    I plan to perform energy minimization of an enzyme with cofactor after homology modeling. In order to process the HETATM records in PDF file, I tried the trp_drug tutor these days. However there were some problems confused me.

1. After the "editconf -bt octahedron -f trp.gro -o trp.gro -c -d 0.5", the "genbox -cp trp.gro -cs spc216.gro -o trp_b4ion.gro -p trp.top" will cause the error of "can not alloc memory"

2. If I use the default tric box, the following genbox will be ok. But when I add 9 Cl- to box by "genion -s trp_b4ion.tpr -o trp_b4em.gro -nname Cl -nn 9 -g trp_ion.log" the program will abort with the error of "Segmentation fault".

    My system is PIII-600, 640M memory, Red hat 7.3. I installed the suggested rpm packages of gromacs (3.2) and fftw (2.1.3). And the demos of water and speptide can be performed correctly. According to the gro file of my sample, the apoenzyme has 1774 atoms and cofactor has 63 atoms.
    Besides, I don't have MOE. So I separated the original PDB file by deepView. After the "editconf" (with tric box), I observed the trp.gro by VDM and found the enzyme/drg are separated greatly. It seems that the drug component doesn't keep the original coordinates of PDB. When I open the gro file of drug (generated from PRODRG[2] server), the VDM can observe nothing.

   In a word, is there some problems with my system or my operations? Any suggestions are welcome, and thank you in advance.

 LI, Jiang

 Kitagawa group
 Okazaki Institute for Integrative Bioscience
 National Institutes of Natural Sciences
 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan 

 EMAIL: jiang-li at ims.ac.jp

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