[gmx-users] Setting custom atoms in FF

[Alex]

I am not sure if your answer was a resounding "yes".
I am talking about the label on the left in PDB.

Let us say I want to name my atoms "TEST1" and "TEST2" and set up my
PDB as

ATOM      1  TEST1   CNT A   1       xxx  yyy   zzz  1.00  0.00
ATOM      2  TEST2   CNT A   1       xxx  yyy   zzz  1.00  0.00

and then in atomname2type.a2t I put

TEST1   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
TEST2   opls_1001   0.1    12.011  3    C  0.142  C 0.142  C 0.149

will the resulting topology contain the distinction despite the issue with bond
lengths? If not, what would be the correct syntax to do that?

I just want to define my atoms in a way that supplements (actually,
precedes) what x2top does when the atoms are not specifically labeled.
A tedious solution in my case, but definitely viable, if this works.

Thank you,

Alex



JL> On 3/29/15 7:53 PM, Alex wrote:
>> Another question about x2top: in the previous discussion, the atom
>> type was determined from its environment and the element type. What if
>> I set up my PDB with atom labels (i think that's the third field from
>> the left in the PDB format), say CJ1 and CJ2 (instead of just C), while the
>> force field contains
>>
>> CJ1   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
>> CJ2   opls_1001   0.1    12.011  3    C  0.142  C 0.142  C 0.149
>>
>> Will then the right distinction be made? I'm asking before trying
>> it, because it is quite tedious for me to do the labeling. The
>> issue is way beyond carbons, I just discovered that a bunch of
>> different atoms isn't set up correctly.
>>

JL> The element field can be up to 16 characters long, per the code (overkill, but
JL> it indicates that there should be some flexibility).

JL> -Justin

JL> -- 
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JL> Justin A. Lemkul, Ph.D.
JL> Ruth L. Kirschstein NRSA Postdoctoral Fellow

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-- 
Best regards,
 Alex                            mailto:nedomacho at gmail.com