Dear Srinivs,
thank you for response. You are right I have already found the source of problem. I have used PEO to name the chain group and forgot that the same group holded for residues.
Greetings
Zuzana
Dňa 03/19/10, jampani srinivas <[email protected]> napísal:
thank you for response. You are right I have already found the source of problem. I have used PEO to name the chain group and forgot that the same group holded for residues.
Greetings
Zuzana
Dňa 03/19/10, jampani srinivas <[email protected]> napísal:
Dear Zuzana,Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from both groups.Srinivs.On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova <[email protected]> wrote:
Dear GROMACS users,
I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong.
I want to compile a PEO chain centered in box of 2900 water molecules.
In my md.mdp the relevant section is as follows
Tcoupl = nose-hoover
tc-grps = PEO SOL
tau_t = 0.1 0.1
ref_t = 50 50
gen_vel = yes
gen_temp = 50 50
I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using
grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50K
and got message
Program grompp, VERSION 4.0.3
Source code file: readir.c, line: 1050
Fatal error:
16 atoms are not part of any of the T-Coupling groups
I tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same.
I would be really thankful for an advice which can move me further. Thank you in advance.
Zuzana
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J. Srinivasa Rao Ph.D.
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
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