hi all i`m new to gromacs and am tyring to simulate a dna molecule. but i am facing following problem on running pdb2gmx
********A PORTION OF OUTPUT******** WARNING: atom H41 is missing in residue DCYT 47 in the pdb file You might need to add atom H41 to the hydrogen database of residue DCYT in the file ff???.hdb (see the manual) WARNING: atom H42 is missing in residue DCYT 47 in the pdb file You might need to add atom H42 to the hydrogen database of residue DCYT in the file ff???.hdb (see the manual) WARNING: atom H41 is missing in residue DCYT 48 in the pdb file You might need to add atom H41 to the hydrogen database of residue DCYT in the file ff???.hdb (see the manual) WARNING: atom H42 is missing in residue DCYT 48 in the pdb file You might need to add atom H42 to the hydrogen database of residue DCYT in the file ff???.hdb (see the manual) ------------------------------------------------------- Program pdb2gmx, VERSION 3.3 Source code file: pdb2top.c, line: 697 Fatal error: There were 102 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing ------------------------------------------------------- kindly help me solve this problem regards, Manish Datt Research Scholar Bioinformatics Centre Institute of Microbial Technology Sector 39A, Chandigarh-160036 India. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php