hi,<br><br>I am simulating a protein complex. The peptide in the complex has PRO at the N-terminal.<br>I run pdb2gmx and choose PRO-NH as the cap for the respective N-terminal.<br><br>pdb2gmx_4mpi -f xyz.pdb -o -ter -ignh -o conf.gro <br>
<br>Select N-terminus type (start)<br> 0: PRO-NH2+<br> 1: PRO-NH<br> 2: NH3+<br> 3: None<br>1<br>N-terminus: PRO-NH<br><br>Then I follow the following steps:<br><br>editconf_4mpi -f conf.gro -bt cubic -d 1.5 -c -o out.gro<br>
<br>genbox_4mpi -cp out.gro -cs spc216.gro -o solvated.gro -p topol.top <br><br>grompp_4mpi -f xyz.mdp -c solvated.gro -p topol.top -o xyz.tpr<br><br>grompp displays the following error:<br><br>ERROR 1 [file topol_B.itp, line 1283]:<br>
No default Proper Dih. types<br><br>**following is line 1283 of topol_B.itp:<br><br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br> 6 1 3 4 1 #THIS IS EMPTY<br>
3 1 6 5 1 gd_19<br> 1 3 4 5 1 gd_17<br> 1 3 7 9 1 gd_20<br> 3 4 5 6 1 gd_17<br><br>Atoms 1-6 come from the terminal PRO and are defined like this in the topology:<br>
<br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 N 1 PRO N 1 -0.28 14.0067 ; qtot -0.28<br> 2 H 1 PRO H 1 0.28 1.008 ; qtot 0<br>
3 CH1 1 PRO CA 2 0 13.019 ; qtot 0<br> 4 CH2 1 PRO CB 2 0 14.027 ; qtot 0<br> 5 CH2 1 PRO CG 3 0 14.027 ; qtot 0<br>
6 CH2 1 PRO CD 3 0 14.027 ; qtot 0<br> 7 C 1 PRO C 4 0.38 12.011 ; qtot 0.38<br> 8 O 1 PRO O 4 -0.38 15.9994 ; qtot 0<br>
<br><br>Now I do not encounter this problem when I choose PRO-NH2+ as the N-terminal cap. The diehedral is defined for NH2+ cap.<br>I am unable to understand that why grompp gives a diehedral error for PRO-NH and everything is fine if I use PRO-NH2+.<br>
<br>Any help that how can I overcome this problem if I want to use PRO-NH as N-terminal cap.<br><br><br><br>Thanks,<br><br>Vivek,<br>Graduate Student,<br>IITK.<br> <br><br><br> <br><br><br><br><br><br><br>