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

2013-09-22 Thread Justin Lemkul
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

2013-09-22 Thread Nilesh Dhumal
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

2013-09-22 Thread Justin Lemkul
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

2013-09-22 Thread Nilesh Dhumal
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

2013-09-22 Thread Justin Lemkul
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

2013-09-22 Thread Justin Lemkul
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

2013-09-22 Thread Nilesh Dhumal
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