[gmx-users] Problem simulating DNA

[Manish Datt]

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.