HI, When I use the merge command along with pdb2gmx to form inter disulphide bonds between two different chains, its removing a water molecule to connect the two ends. Its like forming a peptide bond which I dont wish. Is there any way to tell to gromacs, to create the inter dishulphide bonds without creating the peptide bond between the two chains ?
On Fri, Jun 27, 2008 at 6:51 PM, rams rams <[EMAIL PROTECTED]> wrote: > Hi, > > I have three di sulphide bonds in my crystal structure. In the topology > file it left blanks at the corresponding sulphur connectivities (i.e., > values corresponding to gb_, ga_. gd_ ). When I try to create the .tpr file > it complains the following: > > processing topology... > Generated 716 of the 2628 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 1046 of the 2628 1-4 parameter combinations > WARNING 1 [file "insu_pwi.top", line 607]: > No default G96Bond types, using zeroes > WARNING 2 [file "insu_pwi.top", line 745]: > No default G96Bond types, using zeroes > WARNING 3 [file "insu_pwi.top", line 2008]: > No default G96Angle types, using zeroes > WARNING 4 [file "insu_pwi.top", line 2209]: > No default G96Angle types, using zeroes > WARNING 5 [file "insu_pwi.top", line 2345]: > No default G96Angle types, using zeroes > WARNING 6 [file "insu_pwi.top", line 2512]: > No default G96Angle types, using zeroes > WARNING 7 [file "insu_pwi.top", line 2748]: > No default Proper Dih. types, using zeroes > WARNING 8 [file "insu_pwi.top", line 2820]: > No default Proper Dih. types, using zeroes > WARNING 9 [file "insu_pwi.top", line 2863]: > No default Proper Dih. types, using zeroes > WARNING 10 [file "insu_pwi.top", line 2919]: > No default Proper Dih. types, using zeroes > Cleaning up temporary file gromppID2O6e > ------------------------------------------------------- > Program grompp, VERSION 3.3.1 > Source code file: fatal.c, line: 416 > > Fatal error: > Too many warnings, /usr/local2/gromacs/bin/grompp terminated > ------------------------------------------------------- > > "Encountered Subspace Anomaly" (Star Trek) > > MD_insu.tpr was not created. Check for errors. Exiting ... > > Is there a way to fix it ? Also what are those b_, ga_. gd_ corresponds to > ?? > > Ram. > >
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