Re: [gmx-users] First Energy Minimization in a MD

2012-05-12 Thread Justin A. Lemkul
On 5/12/12 4:25 PM, Lara Bunte wrote: Hello I read the mdp options more than once but I don't understand how to make a good em.mdp file for the first energy minimization, if you plug your molecule in a water box. In my tutorial is this example given. integrator = steep nsteps = 200 This i

[gmx-users] First Energy Minimization in a MD

2012-05-12 Thread Lara Bunte
Hello I read the mdp options more than once but I don't understand how to make a good em.mdp file for the first energy minimization, if you plug your molecule in a water box. In my tutorial is this example given. integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulom

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

2012-05-12 Thread Shima Arasteh
All right. Thank you Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Saturday, May 12, 2012 10:36 PM Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs On 5/12/12 2:00 PM, Shima Araste

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

2012-05-12 Thread Shima Arasteh
Thanks for your suggestions. The total charge is zero in real but what I got through swissparam is as below: [ atoms ] ; nr type resnr resid atom cgnr charge mass    1 C=O  1  LIG C   1  0.4500  12.0110    2 O=C  1  LIG O   2 -0.5700  15.9994    3 HCMM 1  LIG H1  3  0.0600   1.0

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

2012-05-12 Thread Justin A. Lemkul
On 5/12/12 2:00 PM, Shima Arasteh wrote: The total charge is zero in real but what I got through swissparam is as below: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 C=O 1 LIG C 1 0.4500 12.0110 2 O=C 1 LIG O 2 -0.5700 15.9994 3 HCMM 1 LIG H1 3 0.0600 1.0079 4 HCMM 1 LIG H2 4 0.0600

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

2012-05-12 Thread Shima Arasteh
The total charge is zero in real but what I got through swissparam is as below: [ atoms ] ; nr type resnr resid atom cgnr charge mass    1 C=O  1  LIG C   1  0.4500  12.0110    2 O=C  1  LIG O   2 -0.5700  15.9994    3 HCMM 1  LIG H1  3  0.0600   1.0079    4 HCMM 1  LIG H2  4

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

2012-05-12 Thread Justin A. Lemkul
On 5/12/12 1:37 PM, Justin A. Lemkul wrote: On 5/12/12 1:32 PM, Shima Arasteh wrote: Dear gmx users, I want to simulate a peptide in water. The peptide has a formyl residue as the N-terminus. I got the parameters of it and then add it to the .rtp file of charmm36.ff as below: [ For ] [ ato

Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

2012-05-12 Thread Justin A. Lemkul
On 5/12/12 1:32 PM, Shima Arasteh wrote: Dear gmx users, I want to simulate a peptide in water. The peptide has a formyl residue as the N-terminus. I got the parameters of it and then add it to the .rtp file of charmm36.ff as below: [ For ] [ atoms ] ; name type charge chargegroup C C 0.4500

[gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

2012-05-12 Thread Shima Arasteh
Dear gmx users, I  want to simulate a peptide in water. The peptide has a formyl residue as the N-terminus. I got the parameters of it and then add it to the .rtp file of charmm36.ff  as below: [ For ]  [ atoms ] ;  name    type   charge   chargegroup     C  C  0.4500   0