Re: [gmx-users] Re: No such moleculetype SOL

On 9/22/13 10:10 PM, Jonathan Saboury wrote: Then something is wrong with the way you've done it, because the job of spc.itp is to define the [moleculetype] SOL and all its relevant parameters. Hm...not sure what the matter is. Added a forcefield as well as spc.itp to the .top file made by

[gmx-users] Re: No such moleculetype SOL

>Then something is wrong with the way you've done it, because the job of spc.itp >is to define the [moleculetype] SOL and all its relevant parameters. Hm...not sure what the matter is. Added a forcefield as well as spc.itp to the .top file made by acpype. Still getting the error "Fatal error: No s

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

On 9/22/13 9:32 PM, Nilesh Dhumal wrote: Thanks. I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI and 2 ETS. How can I define for 128 EMI and 128 ETS ? List 128 EMI consecutively, followed by 128 ETS consecutively, and make a [molecules] directive analogously. -Ju

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Thanks. I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI and 2 ETS. How can I define for 128 EMI and 128 ETS ? Nilesh > > On 9/22/13 9:18 PM, Nilesh Dhumal wrote: >> Sorry to paste big files here. (.pdb file and processed.top ) >> >> >> pdb file. >> >> TITLE Protein >>

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

On 9/22/13 9:18 PM, Nilesh Dhumal wrote: Sorry to paste big files here. (.pdb file and processed.top ) pdb file. TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Sorry to paste big files here. (.pdb file and processed.top ) pdb file. TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 ATOM 2 C2 E

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

On 9/22/13 8:54 PM, Nilesh Dhumal wrote: Sorry to send email directly to your email address. Because of attachments it not going through gmx_users. The proper protocol is to post the files via publicly accessible URL so that anyone interested in helping may assist. attached the topology

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

On 9/22/13 7:13 PM, Nilesh Dhumal wrote: Hello, I am doing energy minimization for my system. I am getting following warnings Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20) Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21) Warning: atom name 22 in p2.t

[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Hello, I am doing energy minimization for my system. I am getting following warnings Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20) Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21) Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22) Warni

Re: [gmx-users] restarting the crashed run

No, because then the state.cpt file would be redundant :-) All you can do re-start from the beginning, because the .tpr file only has the initial state. You can "extend" the number of steps, but you can't magically produce the state after the first simulation just from the initial one. (If you can,

Re: [gmx-users] restarting the crashed run

Thank you Justin for your reply. Pt 3 should be the correct way to proceed. But somehow if I have lost my state.cpt file, can I continue my run using following commands: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene