[gmx-users] My problem is How to define 5-methyl cytosine by amberff port in gromacs?

Mark Abraham Mark.Abraham at anu.edu.au
Sun May 29 12:47:58 CEST 2011

On 29/05/2011 7:29 PM, Masomeh Dehghani wrote:
> Hi all
> I have inserted a new residue (DM instead of 5CM) and changed relative 
> files(dna.rtp,dna.r2b,dna.hdb,dna.arn ,residutypes.dat,defselection.dat),
> but I have fatal erorrs in grompp:
> {erorr1:[file epo0003-DNA-chain-A.itp ,line 2322]:
> No default Angletypes}
> {erorr2:[file epo0003-DNA-chain-A.itp ,line 3679]:
> No default Improper Dih.types}
> {erorr3:[file epo0003-DNA-chain-B.itp ,line 2322]:
> No default Angletypes}
> {erorr4:[file epo0003-DNA-chain-B.itp ,line 3679]:
> No default Improper Dih.types}//
> anyhelp is greatly appreciate!//

As I said last time, you need to look at those lines in your molecule 
.itp file and see why they don't match the type definitions in your 
forcefield .itp files.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110529/3c90cd03/attachment.html>

More information about the gromacs.org_gmx-users mailing list