<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear All,<br><br>I have a problem when I use ACE patch in one of my proteins using FFG43a1.<br><br>I am issuing:<br>pdb2gmx_3.3 -f test.pdb -ter -ignh -o test.gro<br><br>I am using -ter because I already have ACE at N terminus and NH2 at C-terminus. <br><br>I used this test.gro and put it in a water box and went ahead with editconf and all and finally when I made the test.tpr file using grompp then it reported a warning mesg which is as follows:<br><br>warning: [file "test.itp" , line 5010]<br>No default G96Angle types, using zeroes.<br><br>Now when I check the line 5010 it is:<br><br>[ angles ]<br>; ai aj ak funct
c0 c1 c2 c3<br> 1 2 3 2 <br> 1 2 4 2 ga_18<br> 3 2 4 2 ga_32<br><br>Now the first line is the line 5010 and it is nothing but the angle parameter of CH3-C-O of ACE group. As is observed here no ga_ is defined in front of line 5010. I also checked the .rtp file and there too this angle parameter is undefined. <br><br>[ ACE ]<br> [ atoms ]<br> CA CH3 0.000 0<br>
C C 0.380 1<br> O O -0.380 1<br> [ bonds ]<br> C CA gb_26<br> C O gb_4<br> C +N gb_9<br> [ angles ]<br> CA C +N ga_18<br> O C +N ga_32<br> [ impropers ]<br> C CA +N O gi_1 <br><br>Although if I proceed with it then there is no problem and my simulations (production run) are running fine, but I am just curious to know why is this happening. I tried using difference force fields from pdb2gmx but all
of them give me the same problem.<br><br>Another thing is, is it correct to ignore this warning message since it is for a patch only?<br><br>I shall be really thankful if I would be getting your useful suggestions on this issue.<br><br>Priyanka<br></div></div><br>
<!--2--><hr size=1></hr> Unlimited freedom, unlimited storage. <a href="http://in.rd.yahoo.com/tagline_mail_2/*http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/">Get it now</a></body></html>