Re: [gmx-users] DNA topology error

On 7/11/17 3:40 PM, maria khan wrote: dear Mark Abraham According to my error like """Residue 9 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom O5' used in that entry is not found in the input file. Perhaps your atom and/or residue

[gmx-users] DNA topology error

dear Mark Abraham According to my error like """Residue 9 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom O5' used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.""" if O5' can be set

Re: [gmx-users] DNa topology error.

Hi, pdb2gmx found a residue called DG and found an rtp entry that matched it. It just didn't find an O5' atom within it. You should also be able to find that residue. Mark On Tue, Jul 11, 2017 at 5:26 PM maria khan wrote: > Thanks Mark Abraham. > > i would like to

[gmx-users] DNa topology error.

Thanks Mark Abraham. i would like to share my pdb file as still i dont understand the error as well as your answer,kindly look at this then explain it. it cant be shared as the file is large.i checked the file in front of residue 9,there is no DG at all .All along the chains is DA. regards. --