Re: Re: [gmx-users] Difference in the Forcefields and speed...

Hello, Thankyou Drs Mark Abraham and Caterina Arcangeli for the useful suggestions. They worked for me. I could cat the two trr files and calculate the backbone g_rms values. I have to yet see how much they deviate with the original structures. I have couple of q

Re: [gmx-users] Error in .top file for grompp

한상화 wrote: > Dear Gromacs users, > > > > I have gone through all the way to the final product MD, where I > received the following error message for grompp. > > The same topology file pn.top did not give me any problem in the > previous steps including grompp with pr.mdp or grompp with em.md

[gmx-users] Error in .top file for grompp

Dear Gromacs users, I have gone through all the way to the final product MD, where I received the following error message for grompp. The same topology file pn.top did not give me any problem in the previous steps including grompp with pr.mdp or grompp with em.mdp. I included solvent and ions

Re: [gmx-users] Error when adding a unnatural amio acid

Please email me offline your pdb and rtp file. I will see how to resolve this issue. Regards, Yang Ye On 1/4/2007 7:23 AM, yuemin liu wrote: This is a good idea. But here comes following major complaints: "Atom H4 not found in rtp database in residue ASO, it looks a bit like H1". Does the grou

Re: [gmx-users] Error when adding a unnatural amio acid

Please send me directly your pdb and rtp file. I will see how to resolve this issue. Regards, Yang Ye On 1/4/2007 7:23 AM, yuemin liu wrote: This is a good idea. But here comes following major complaints: "Atom H4 not found in rtp database in residue ASO, it looks a bit like H1". Does the group

Re: [gmx-users] Error when adding a unnatural amio acid

This is a good idea. But here comes following major complaints: "Atom H4 not found in rtp database in residue ASO, it looks a bit like H1". Does the group number matters? I assigned the bulky side chain as one group number 4. Should the H4 comes with O4? I check my rtp file, O4 is connected to C4 a

Re: [gmx-users] Error when adding a unnatural amio acid

To debug this problem. I suggest you to create a pdb file which contains only ASO residue and play with pdb2gmx. Regards, Yang Ye On 1/4/2007 1:26 AM, yuemin liu wrote: It does not work either. Thanks anyway. I doubt the error results from sth else. Most likely the reason is default angle and

Re: [gmx-users] Error when adding a unnatural amio acid

It does not work either. Thanks anyway. I doubt the error results from sth else. Most likely the reason is default angle and dihedral values in the modified ffgmxbon.itp file. By the way, how would you assign default angle and dihedral values? Structurally it is fine unless the size matters, becaus

Re: [gmx-users] Error when adding a unnatural amio acid

Hi, You may try Dr Mu's suggestion: check file xlateat.dat and find any line matching protein XXX H1 XXX could be any name of an atom. Remove this line and decrement the number on the top. Regards, Yang Ye On 1/3/2007 11:18 PM, yuemin liu wrote: I did add the resname in aminoacids.dat an

Re: [gmx-users] Error when adding a unnatural amio acid

I did add the resname in aminoacids.dat and also change the the number on the top. It still complains same thing. It is H atom type also name H (connecting to N) in the new amino acid like the regular amino acid, and has nothing to do with H1 at all. Thanks, Liu, Yuemin --- Yang Ye <[EMAIL PROT

Re: [gmx-users] Error when adding a unnatural amio acid

Thanks and Happy New Year! Wishes, Liu, Yuemin --- Yang Ye <[EMAIL PROTECTED]> wrote: > You may try add residue name ASO to the end of > /top/aminoacids.dat and > also increment the number on the top. > > Regards, > Yang Ye > > On 1/3/2007 8:55 AM, yuemin liu wrote: > > Hi, Everyone, > > > >

Re: [gmx-users] Can I use more memory to speed up computa tion?

Hi, There is no point for this "optimization" in the case of MD and GROMACS. MD doesn't occupy much memory because for each atom, only six variables (three coordinates and three velocities) are needed. Program code isn't that complex, too. Except you have a on-die cache like this large, memory siz

Re: [gmx-users] pdb for a structure with more then 300 atoms

nur avneet wrote: Dear all I have a peptoid sequence (peptoids have the amino acid side chain appended to the amide nitrogen rather then alpha carbon) with more then 300 atoms. Please guide me an easy way to generate its pdb or gromacs coordinate and topology files, as PRODRG server doesnt wor

[gmx-users] pdb for a structure with more then 300 atoms

Dear all I have a peptoid sequence (peptoids have the amino acid side chain appended to the amide nitrogen rather then alpha carbon) with more then 300 atoms. Please guide me an easy way to generate its pdb or gromacs coordinate and topology files, as PRODRG server doesnt work for more then 300

Re: [gmx-users] (no subject)

Hi, using the command: trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -o nchnp3_15pep.trr -settime the program will ask you the start time of each file. Try putting "5001" for the first file and "c" (continue) for the second file. It should be work. Ciao Caterina Mark Abraham wrote: > sharada wr

Re: [gmx-users] (no subject)

sharada wrote: Hello gmx_users, I wish you a very happy and prosperous new year 2007. I have a very fundamental question in trjcat usage. I have two *.trr files of 5ns and 10 ns runs . I would like to concanate the two and make a 15ns trr file. How to give the command so that the starting t

[gmx-users] (no subject)

Hello gmx_users, I wish you a very happy and prosperous new year 2007. I have a very fundamental question in trjcat usage. I have two *.trr files of 5ns and 10 ns runs . I would like to concanate the two and make a 15ns trr file. How to give the command so that the starting time of the 10ns fi