[gmx-users] Too close water molecules.

saurabh shakya shakya_79 at yahoo.com
Thu Jan 8 13:53:01 CET 2004

Hello Dr David,
I tried running pdb2gmx with the addtions to
specbond.dat as you suggested and it runs successfully
now ,thanks for your help . However now I am running
into another problem ...as the cystines are bound to
Fe i have calculated the charges on the iron sulfur
cluster  and the 4 cystines ,the charges on cystine
are as follows 
    6 N           -0.4821
    7 H            0.218549
    8 Ca            0.702265
    9 Ha          -0.071973
   10 Cb           -0.276902
   11 Hb           0.196618
   12 Hb            0.062929
   13 Sg           0.006376
   14 C           0.200239
   15 O          -0.275707

Now when i am trying to use these charges in the force
field (oplsaa) i am again running into lincs warning
for the different atoms of cystine like Cb-Hb ,Cb-Ca
.Is it ok to alter the charges in the forcefield ? 


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