Re: [gmx-users] problem in simulation of dna-protein complex

Hi Nitu, Check the atoms and their order in the pdb and the rtp file and try to find out which match and which miss. >     C2    amber99_2 0.56770    25 > O    amber99_41   -0.58810    26 I place my bet on this one. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) B

[gmx-users] problem in simulation of dna-protein complex

Dear all I am doing simulation of DNA -protein complex using amber port with gromacs-4.0.3 . for this I have to make changes in my .pdb file a/c to entry in .rtp file of amber force field. I have all possible changes but when I run the pdb2gmx command the error came lik

Re: [gmx-users] problem in simulation of dna-protein complex

nitu sharma wrote: Dear all , I am doing simulation of DNA-protein complex. Is anybody have idea about .hdb of DNA becoz in mannual nothing is wrritten about DNA hydrogen database .I have edited The database like this- ADE 9 2 6 H5* C5* C4* O

[gmx-users] problem in simulation of dna-protein complex

Dear all , I am doing simulation of DNA-protein complex. Is anybody have idea about .hdb of DNA becoz in mannual nothing is wrritten about DNA hydrogen database .I have edited The database like this- ADE 9 2 6 H5* C5* C4* O5* 1 5 H4* C4*

RE: [gmx-users] problem in simulation of DNA-protein complex

@gromacs.org Subject: [gmx-users] problem in simulation of DNA-protein complex Dear all I am getting problem in running pdb2gmx command on DNA_protein file . The prblem is Program pdb2gmx, VERSION 4.0.3 Source code file

Re: [gmx-users] problem in simulation of DNA-protein complex

nitu sharma wrote: Dear all I am getting problem in running pdb2gmx command on DNA_protein file . The prblem is Program pdb2gmx, VERSION 4.0.3 Source code file: resall.c, line: 426 Fatal error: Residue 'T' not foun

[gmx-users] problem in simulation of DNA-protein complex

Dear all I am getting problem in running pdb2gmx command on DNA_protein file . The prblem is Program pdb2gmx, VERSION 4.0.3 Source code file: resall.c, line: 426 Fatal error: Residue 'T' not found in residue topology da