Re: [gmx-users] pdb2gmx : treat CL as C

Nilesh Dhumal wrote: Tsjerk, When I open di.pdb (output file) in VMD. I see all CL are repalced by C. I can't go to next step. What information do you want more. I checked the format of pdb file again. Its looks dioxin.pdb is ok. After running pdb2gmx, the di.pdb output file don't have any CL

Re: [gmx-users] pdb2gmx : treat CL as C

Tsjerk, When I open di.pdb (output file) in VMD. I see all CL are repalced by C. I can't go to next step. What information do you want more. I checked the format of pdb file again. Its looks dioxin.pdb is ok. After running pdb2gmx, the di.pdb output file don't have any CL atom. Hopes you get me n

Re: [gmx-users] pdb2gmx : treat CL as C

Oops, there's an .rtp entry. Shame on me :$ Maybe a good idea though to post the output of pdb2gmx. Cheers, Tsjerk On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar wrote: > Justin, > >> What is the problem?  It looks like you got everything to work, but the .pdb >> file you've posted is misfor

Re: [gmx-users] pdb2gmx : treat CL as C

Justin, > What is the problem?  It looks like you got everything to work, but the .pdb > file you've posted is misformatted on the CL lines: > > ATOM     14  C14 PCD     1      -2.372  -1.395   0.000  1.00  0.00 > C > ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00 >  CL > > Not

Re: [gmx-users] pdb2gmx : treat CL as C

Nilesh Dhumal wrote: here is all information. I attached 2 attachment to my privious mail. It looks 2nd didn't come. Sorry. Here I am giving details. I am using opls force field . I added "PCD" as residue name in aminoacid.dat file. pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter i have atta

Re: [gmx-users] pdb2gmx : treat CL as C

here is all information. I attached 2 attachment to my privious mail. It looks 2nd didn't come. Sorry. Here I am giving details. I am using opls force field . I added "PCD" as residue name in aminoacid.dat file. pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter i have attached input:dioxin.pdb, ou

Re: [gmx-users] pdb2gmx : treat CL as C

Nilesh Dhumal wrote: this is the command, pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter Here I have attached the dioxin.pdb file. IN di.pbd there is no CL atoms. I asked for your inputs and outputs. You haven't told me which forcefield you input or anything about what pdb2gmx wrote as outp

Re: [gmx-users] pdb2gmx : treat CL as C

2009/11/17 Nilesh Dhumal > this is the command, > > pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter > > Here I have attached the dioxin.pdb file. > Check your dioxing.pdb.. there might be formatting issues. It might happen the due to bad format of the pdb file, your 'L' is somehow removed from 'C

Re: [gmx-users] pdb2gmx : treat CL as C

this is the command, pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter Here I have attached the dioxin.pdb file. IN di.pbd there is no CL atoms. NIleshREMARK Accelrys Discovery Studio PDB file REMARK Created: Sat Nov 14 17:45:28 Eastern Standard Time 2009 ATOM 1 O1 PCD 1 0.000

Re: [gmx-users] pdb2gmx : treat CL as C

Nilesh Dhumal wrote: Hello, My system is having chlorin atoms. Duing pdb2gmx it treat Chlorne atoms as carbon. Can you tell me where is the problem. Is there any prblem in my pdb file The problem could be in any number of places, and you've not told us enough about your simulation system, comm

Re: [gmx-users] pdb2gmx : treat CL as C

Nilesh The atom type C is for Carbon and for chlorine is Cl. So, substitute Chlorine's atom type with Cl. Chandan On Tue, Nov 17, 2009 at 9:04 AM, Nilesh Dhumal wrote: > Hello, > My system is having chlorin atoms. Duing pdb2gmx it treat Chlorne atoms as > carbon. > Can you tell me where is the

[gmx-users] pdb2gmx : treat CL as C

Hello, My system is having chlorin atoms. Duing pdb2gmx it treat Chlorne atoms as carbon. Can you tell me where is the problem. Is there any prblem in my pdb file Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi