Re: [gmx-users] error in phosphoserine simulation during MD

Hi, You need to use a tool capable of doing the job. But it is unclear to anyone reading this how phosphoserine relates to the problem, or what loop needs to be built. Mark On Sun, 18 Jun 2017 22:07 marzieh dehghan wrote: > thank you very much > > I tried to complete

[gmx-users] error in phosphoserine simulation during MD

thank you very much I tried to complete pdb file, but since pdb file containing phosphoserine which is different from its sequence, because there is serine in its sequence file, when I wanted to use modeller, I confronted these error " sequence difference between alignment and pdb. I used

Re: [gmx-users] error in phosphoserine simulation during MD

On 6/18/17 2:19 PM, marzieh dehghan wrote: Hi Dear Justin Thanks a lot for your kind answer, I applied two types of command to get rid of the previous error *at first*, the following command was used: *gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc * but I confronted these

[gmx-users] error in phosphoserine simulation during MD

Hi Dear Justin Thanks a lot for your kind answer, I applied two types of command to get rid of the previous error *at first*, the following command was used: *gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc * but I confronted these error CYS901 SG7090 1.414 CYS905 SG7117

Re: [gmx-users] error in phosphoserine simulation during MD

On 6/17/17 4:05 PM, marzieh dehghan wrote: Hi Dear all I want to simulate a protein containing phosphoserine using MD, so I place the force field into the working directory and modified all parameters of force field for example SEP (phosphoserine) was added as Protein in the

[gmx-users] error in phosphoserine simulation during MD

Hi Dear all I want to simulate a protein containing phosphoserine using MD, so I place the force field into the working directory and modified all parameters of force field for example SEP (phosphoserine) was added as Protein in the residuestypes.dat , but I confronted the following error? Atom